The Doctor Is In
by Doctor poo and the TURDIS
Summary: The Time Lord known as the Doctor has just lost the Ponds in Manhattan. In a bid to lift his spirits, the TARDIS takes him to another universe, one where its inhabitants have never heard of him. But with omnicidal machines threatening the galaxy, it seems the Time Lord will fall back into an old habit he's been trying to shake since that fateful day.
1. Foreword

_Shepherd; one who offers guidance or leadership._

 _We get that word from Her, you know._

 _The Shepard, the one who vanquished the Reapers, who drove the Andromedans back to their own galaxy, who served as a bridge between the races of the Milky Way, and the Time Lords of old. Shepard is almost universally recognized as a hero, a herculean type figure of epic stature, but she didn't start out that way, oh no._

 _Shepard was born in- well, nobody really knows when she was born, except for her father, but in the interest of time, let's just say she was born in 2158, and leave it at that._

 _Shepard was raised by Captain Hannah Shepard of the Alliance Navy, moving from ship to ship, never staying for too long._ _Shepard finally enlisted with the Alliance Navy at the age of eighteen, as part of a desire to, in her own words, "Make mommy proud."_

 _I think she succeeded in that department, don't you?_

 _Shepard had a... difficult career, to say the least. Elysium, the colony she had been stationed on, was attacked by a gang of ruthless pirates and slavers from the Terminus Systems. Shepard succeeded in defending the colony... at the expense of over half her squad. But the incident proved her worth to the Alliance, and she was bumped up to the advanced training course._

 _The N7 Program, as it's also known._

 _Shepard nearly flunked out of the training several times, not an uncommon occurrence, given the difficulty of the program, but what did make it uncommon, was Shepard's tenacity._

 _"She never gives up._ _ **Ever.**_ _" was the phrase I believe one of her instructors used._

 _She eventually completed the program, and went on to perform several classified missions, most of which have become declassified. But even today, almost three-thousand years later, her mission to stop the Collectors, and her exploits to stop the Reaper invasion have been lost to time. Meaning that most of Shepard's exploits are shrouded in myth, misinformation, and outright lies._

 _Hopefully, this can clear that up._

 _I've recently grown... involved with someone who was on Shepard's crew during her mission to stop the Collectors, and later, the Reapers._

 _This is the most complete and accurate account of Shepard's journey that you will find anywhere. Period._

 _Everyone has a different outlook on Shepard, and this doesn't line up with all of them But, nevertheless, I urge you to read on._

 _What you'll find, may surprise you._

-Foreword to A Completely Accurate Account of The Shepard, by Professor River Song.


	2. Prologue

**_So there I was, trying to go to sleep, when a plot bunny started hopping wildly around in the fields of my mind. It kept me awake, and refused to leave me be until I got this wrote up. So, here it is. A little info first: The Doctor in this story is Eleven (I don't feel confident enough in my ability to write any of the other ones just yet) in between the loss of the Ponds and his self-imposed exile to Victorian England._**

 ** _Second, is that, while it may be one of my longest-running projects, and close to being finished, I'm taking a break from the JADIS trilogy, as at the moment, I'm just too burned out on it. But it is by no means apparent._**

 _ **Finally, and this should go without saying, there will be spoilers. Why you're even reading fan fiction about a certain franchise if you barely know anything about it is beyond me.**_

 _ **OBLIGATORY DISCLAIMER: I do not own Doctor Who, or Mass Effect. Those properties belong to the BBC and BioWare, respectively.**_

* * *

The Doctor sat in the newly redecorated TARDIS, silently sulking (though he would never admit it) over the loss of the Ponds. He gently touched Amy's reading glasses that he picked up, looking at them sullenly, as the time rotor's iconic sound reverberated throughout the ship.

 _'Don't you have better things to do, my thief?'_ The TARDIS 'spoke.' The TARDIS never actually spoke any words, except for the encounter on House, but the Doctor could pick up enough of a meaning in the simple waves of emotion the sentient ship sent out.

"No. I'm done." The Doctor responded silently, uncharacteristically honest.

 _'Done with what, pray tell?'_

"Romping around the universe." The Doctor said, still looking down at the glasses, unable to shake the image of Amy vanishing right in front of him. "This universe's had enough of me, I get that now."

 _'You speak as if the universe were a sentient construct.'_

"Might as well be, considering how it seems to loathe me." The Time Lord said, seemingly void of any emotion. "Then again, it could just be a natural law. Gravity makes things fall, time makes things age, and I make things turn to dust."

 _'...Well then, if_ this _universe has had enough of you, then we'll just have to find one that_ hasn't.'

"What do you mean by that?" The Doctor looked up. The time rotor's groaning-wheezing noise suddenly shifted in pitch, as the console room shook uncontrollably. The Doctor launched up from his seat, and ran over to the console. "No, don't do that! I don't remember telling you to do that!"

He furiously pressed every button, flipped every lever end switch, and turned every dial, to no response. He whirled one of the monitors around to face him, and looked upon it with wide eyes. "Hold on, you don't want to-!" He was cut off as a loud bang from the ripping of space and time itself occurred, and the time lord was thrown to the floor.

* * *

 _SSV Normandy_

The Normandy shuddered as it dropped out of FTL.

"Disengaging FTL drives." The Normandy's helmsman, Jeff "Joker" Moreau reported. "Emission sinks active. Board is green, we are running silent."

"Good work." Thea Shepard, the Normandy's Commander, complimented the pilot. "Are there any Geth ships in the vicinity?"

"No, sir." Navigator Charles Pressly said, walking up into the cockpit. "I'm telling you, Commander, we're wasting our time. We've been searching up and down this sector for three days, and there's _still_ no sign of Geth activity."

"Three ships disappeared here last month. Something happened to them." Joker said.

"Commander, there's some pretty odd readings." Private Jones at the targeting station reported.

"Define 'odd.'" Shepard ordered.

"It's a black spot." Jones reported. "The sensors are picking up nothing, _at all._ Anything that goes off in that direction just vanishes. Not even LADAR scans are getting anything."

"How big is it?" Shepard asked.

"Let's see..." Jones tapped a few controls. "It's about twelve feet tall, five feet long, and five feet wide."

"Send the data back to the Alliance." Shepard ordered. "If this is supposed to be some kind of new stealth tech made by the Geth, then the brass needs to know."

"Transmission sent." Jones reported. "Picking up something else, Commander. An unidentified vessel, looks like a cruiser."

"Doesn't look like any cruiser I've ever seen." Shepard peered at the display.

The private's eyes widened. "Cruiser is changing course. It's on an intercept trajectory."

"Can't be." Pressly piped up. "The stealth systems are engaged, there's no way a Geth ship could possibly-"

"It's not the Geth!" Joker shouted in realization. "Brace for evasive maneuvers!"

The people inside the ship teetered uncontrollably as Joker tried to get the Normandy out of the path of the unknown ship. He was unsuccessful, as a beam weapon of some kind completely overwhelmed the kinetic barriers, and sliced right through the hull of the ship.

An explosion knocked Pressly to the floor as the ship started to crumble.

"Pressly!" Jones shouted. She got up from her seat, and was too, killed by an exploding console.

"Kinetic barriers down! Multiple hull breaches!" Joker frantically reported. "Weapons offline! Somebody get that fire out!"

Shepard, meanwhile, ran as fast as her legs could carry her. She sprinted down the stairs to deck 2, and ran over to the emergency control panel, located at the end of the corridor containing the sleeping pods.

Debris fell from the ceiling as the Normandy's internal superstructure started to melt and deteriorate.

"Shepard!" Kaidan Alenko, part of the Normandy's marine compliment shouted, as he ran up to the Commander.

"The distress beacon's ready for launch." Shepard said, as she sealed her own helmet.

"Will the Alliance get here in time?" Kaidan asked.

Another fire broke out from behind Shepard, and the Commander ran to grab the extinguisher. "They won't leave us here to die. Get everyone onto the escape shuttles."

"Joker's still in the cockpit." Kaidan said, as he started helping to put out the fires. "I'm not leaving either."

"That was an order, marine!" Shepard pointed. "I'll get Joker out of here." She said, as she grabbed hold of two broken power cables, trying to reconnect them. She looked to the marine behind here, and said: "Kaidan, go. Now."

"Aye, aye, ma'am." Kaidan reluctantly said, as he went off to do as ordered.

Shepard reconnected the two cables, and pressed a button on the control panel. Outside, part of the ship's hull lifted up, exposing the escape shuttles in their launch tubes. Each one of the white rings on the holographic display turned red as each shuttle launched, one-by-one.

Looking at the display, Shepard noted that there was still one escape shuttle, present just behind the cockpit. She checked her suit's seal, and ran through the crumbling Normandy's corridors.

 _"Mayday, mayday, mayday!"_ Joker shouted over the emergency channels. _"This is SSV Normandy! We've suffered heavy damage from an unknown enemy!_ _C'mon baby, hold together, hold together."_ Joker tried to will the ship, as Shepard walked through the door into the CIC.

Or rather, what was left of it. The roof of the ship had been completely torn off, depressurizing the entire deck, and exposing it to the vacuum of space. Shepard ran through the barrier protecting Joker, and ran up to the pilot. "Joker, we have to get out of here!"

"No!" Joker defiantly shouted back. "I'm not abandoning the Normandy, I can still save her!"

Shepard gently grabbed onto Joker. "Jeff, the Normandy's lost. Going down with the ship isn't going to change that."

Joker looked sullen. "Yeah. Okay, help me up."

The two looked through the breach in the CIC, and witnessed the unknown ship closing in again. "They're coming around for another attack!"

Shepard grabbed Joker's arm forcefully, and dragged him up. "Watch the arm!" The pilot shouted in pain.

Joker, supported by Shepard, hobbled over to the escape shuttle located across from the airlock. The helmsman was pushed in, and just when Shepard was also about to board, a large explosion threw Shepard away from the shuttle, and over to the exterior launching mechanism.

"Commander!" Joker shouted in fear.

Shepard didn't take the time to think about herself. "Shepard!" Joker shouted out. The Commander pressed the button, and the shuttle's doors closed, as the shuttle itself launched away.

Another shot from the beam weapon of the unknown lanced through what was left of the Normandy, and Shepard was propelled into the wall by the blast.

Gravity cancelled out as the ship lost what little power his had left, and Shepard floated off into space, as the Normandy died in a final, magnificent explosion.

Shepard floated away, only to realize too late that while she was indeed alive, it wouldn't be that way for much longer.

Bits of shrapnel from the explosion cut through her suit, creating several breaches.

Shepard frantically tried to plug the holes with her hands, in a desperate attempt to stop the oxygen from leaking out.

But it was all for naught, as there were too many leaks, and too much oxygen had already vacated the suit.

Shepard passed out, but before she did, she thought she saw something just _appear_ out of nowhere, with the steady pulsing of a light.

Shepard finally lost consciousness, and fell to the planet below, never knowing what the strange object was.

But (un)fortunately for her, it wouldn't remain that way for long.

* * *

"What's that?" The Doctor muttered to himself, as he looked at the monitor. "A distress signal?" The Doctor looked at the data in front of him, and pushed the monitor away. "Well, whoever it is, it's too late now." The Doctor said, as he started setting course for another planet, possibly even time. "How'd you feel about going to Confectius? I hear the rock candy cliffs look brilliant this time of year." He said, flipping the dematerialization lever.

The time rotor made its iconic sound as the TARDIS flew through the time vortex. The rotor halted, signalling that the TARDIS had landed.

The Doctor peeked out the door, to see that he was most definitely not at his destination.

The Doctor slammed the door, and marched back over to the console. "Does _that_ look like an artificial planet made entirely out of candy to you?"

"You have reached your destination." The TARDIS replied, using a GPS-like voice clip.

"No, I haven't." The Doctor responded. "I asked for the planet of candy, not the galactic garbage heap!" The Doctor went over to the door, and swung it open. "Does that look like..." The Time Lord trailed off, as a species he had never seen before passed by. "Well, that's new." The Time Lord smiled. He went over to the railing, and grabbed the Victorian-style longcoat off the railing, throwing it on. He walked back to the door, and was about to open it again, but he stopped. Didn't he say that he was done with the universe romping?

"Oh, sod it." He mildly cursed. "There's always tomorrow." He opened the door, stepped out, and shut it, taking the time to make sure it was locked.

As he turned around, he was met with a sharp blade.

"Give me your credit chit." A deep, rasping voice commanded.

"My what now?"

"Your credit chit, now!"

"I don't think I want to."

"What?" The mugger demanded. "You give me everything you have right now, or losing your things is going to be the least of your problems."

"See, you're not very consistent. And with a form like that..."

"Form? What form?"

"See, you're a very athletic fellow, yes, but there's no form. You're too stiff, your arm's at least three centimeters down from where it should be, and you're not concentrated. See, if you tried to mug me, I could take the knife out of your hands without breaking a sweat. See?" He said, holding up and looking at the knife in disdain.

"What the-!?" The alien's hands shot upwards. "I-I swear, I didn't mean nothing by it!"

"Of course you didn't." The Doctor remarked. He threw the knife into a nearby trash compactor. "Now, go. Before I change my mind."

"Th-thank you!" The alien shouted as it ran away.

"Brilliant. Not five minutes here and I already have people cowering in fear at me. That's got to be a new record." The Time Lord looked around for any sign as to where or when he was. Fortunately enough, his luck held out, and he quickly spotted a sign with the info that he wanted. "Let's see... Omega Station? July 8th 2186 GCE. Okay, that's definitely new."


	3. Lazarus Research Station - PART I

Shepard groaned as she rubbed her face, feeling deep scars. The last thing she remembered was the Normandy, getting disintegrated.

 _"Wake up, Commander."_ A mysterious voice commanded from overhead.

The Commander's eyes snapped open, and she looked around frantically, trying to gauge where she was.

 _"Shepard, you need to get out of that bed, and moving. This facility is under attack!"_

Complying with the voice, Shepard sat up, clutching at her side as she did so.

 _"There's a pistol in the locker on the other side of the room. Hurry!"_

Shepard planted her feet on the floor, and pushed herself from the table she was on. She ran over to the locker, limping as she did so. She pressed a button on the locker, causing it to slide open, revealing the N7 armor inside, in pieces. Shepard picked up each piece, and put them on, the pieces linking together as more was put on.

Finally, Shepard put on the helmet, and the suit's systems booted up, revealing a little dialogue box.

 _ **/Hardsuit computer initializing... complete**_

 _ **/Heads Up Display online**_

 _ **/Communications interface online**_

 _ **/Kinetic barriers activated**_

 _ **/Medi-gel dispensers online**_

 _ **/Vital sign monitoring activated**_

 _ **/Weapon selection system activated**_

 _ **/Power selection system activated**_

 _ **/Thermal clip monitoring activated**_

 _ **/Have a pleasant day!**_

Okay, that was a bit different than Shepard was used to. Shepard grabbed the pistol, and her suit's computer seemed to link with it, telling Shepard that the pistol didn't have a thermal clip. Whatever that was.

"This pistol doesn't have a thermal clip." Shepard told the voice.

 _"It's a med-bay!"_ The voice overhead seemed frustrated, even though a med-bay with an armor locker made just as much sense. _"We'll get you a clip from..."_ On the other side of the room, the exit door seemed to experience some kind of overload, causing the locking mechanism to violently explode. _"Damn! Shepard, are you alright?"_

"Feeling fine." Shepard coughed, lying through her teeth. Honestly, she felt worse than the time she got hammered at that bachelorette party.

 _"Someone's hacking security trying to kill you."_ The voice explained. _"Grab the thermal clip that's on the floor."_

Shepard did just that, and looked at the clip strangely, trying to study it. Before the Normandy was destroyed, thermal clip based weapons were only in the prototype stages. Obviously, these people had connections.

Shepard spotted a small tube set into the side of the pistol, just large enough to hold the clip, with two protrusions close together in the tube. She lined up the protrusions with two small lines that ran along one side of the clip, and slid it in. Then, Shepard moved into the next room, where several tables were overturned.

 _"It looks like they set up a barricade to try and hold the mechs off."_

Shepard vaulted over the barricade, and spotted a mech at the top of the stairs, which prompted her to duck behind a container.

Shepard popped up from cover after the mech stopped firing, and unleashed her own barrage of bullets at the mech's head, causing it to explode.

Shepard got out from behind the crate, and proceeded into the next room.

 _"Shepard, you've got incoming."_ The voice reported, as around eight mechs came into the room from in front and the left.

Shepard once again ducked into cover. She popped up, releasing an incineration blast from her omni-tool, taking out three of the mechs. The Commander then trained her pistol on another, taking it out with an overload. The last two were easily dealt with by a few well-placed headshots.

She started moving again, through the hallways of the facility. She entered a large room with multiple levels, Shepard being on the top. Across from her, she noticed a large conspicuous symbol. It took her a minute to place it, but she recognized it belonging to Cord-Hislop Aerospace, a starship manufacturing company.

So what the hell was she going in one of their facilities? Something about the whole thing seemed off.

 _"Shepard, a large group of mechs is closing in on your position. Take the grenade launcher off the security officer."_ The voice guided.

Burying her questions, Shepard picked up the weapon in question, and studied it. It only furthered the mystery as to where she was. What kind of aerospace engineering firm needs a grenade launcher?

 _"Here they come, Shepard."_ The voice warned.

A door on the level below Shepard opened, and a large volume of mechs entered. Shepard took aim, and fired. The blast ripped into a gas pipe, igniting the flammable material, and setting fire to every last mech in the room. Shepard holstered the launcher, and took the elevator nearby down to the door.

Shepard sprinted through the flames, her hardsuit protecting her from the flames' heat.

 _"You'r-... -ing gre... -ard. Mak... -ur wa... t... -uttle bay."_ The voice started getting choppy as static cut through the comms. _"-ard? -read me? Mechs are..._

The voice finally cut out, leaving Shepard to fend for herself.

"Crap." Shepard vocalized. The Commander pressed forward, entering a small room that looked like a research lab.

Shepard went over to a terminal in the corner of the room, and activated it.

Immediately, a recording of a raven-haired woman started up. _"Progress is slow, but subject shows signs of recovery."_ The woman on the recording spoke, sharing the same voice as the one who was guiding her just a moment ago. _"Major organs are again functional, and there are signs of rudimentary neurological activity. In an effort to accelerate the process, we've moved from simple organic reconstruction of the subject to bio-synthetic fusion. Initial results show promise."_

Shepard raised an eyebrow in confusion. The scans in the room were all obviously from Shepard, so the woman had to be talking about her, but just how bad was it?

In an effort to find out more, Shepard accessed a different terminal, on the other side of the room. This terminal was full of medical procedures that the Commander didn't have the first clue about. But, that 'Heavy skin weave' thing looked interesting, so she took it. She also hacked into a wall safe, looting the credits, before proceeding on her way.

On her way out, she passed by a window. Peering into the reflective surface, Shepard examined herself. She still had her blonde hair and brown eyes, but as she looked, her round face appeared to be more scarred, and bony and angular in some places, no doubt because of whatever procedures they used to save her.

And her nose was a little bit crooked. She was a bit pissed about that. Shepard shook her head, readied her pistol, and proceeded along through the station.

The Commander walked through the door, into what Shepard thought was an atrium of some kind. An African-American man was ducked behind a low railing, firing on mechs across the gap.

"Shepard?" The man asked in surprise as the Commander approached, crouching down as well. "What are you doing here? You're supposed to be a work-in-progress."

"Look, buddy, I have no idea where I am, or how I got here. You know more than I do at this point."

"Right. Sorry 'bout that." The man apologized. "My name's Jacob Taylor, I've been stationed here for-" Jacob was cut off as a shot from a mech hit the railing, nearly taking off the top of Jacob's head. "Damn it!"

Jacob peeked out, and fired his pistol at two of the mechs, taking them out, before popping back down. "Things must be way worse than I thought if Miranda's got you running around here. I'll fill you in the best I can, but we should probably take care of those mechs first."

"Good plan." Shepard agreed. "Do you have any kind of special abilities?" Shepard inquired, in order to be able to make effective use of Jacob.

"I'm low on thermal clips, but I'm a biotic." Jacob explained. "Just say the word, and I'll give 'em a bit of the good stuff." Jacob said, popping up, and unleashing a biotic pull upon the mechs. Jacob pulled more mechs using his biotics, and Shepard took out the floating automatons using her regular weapons. "They're falling back." Jacob happily reported, holstering his weapons. "You ready to get the hell off this station?"

"I've got some questions, first." Shepard said.

"Understandable." Jacob said. "Ask away."

"What do you do here?"

"Security, mostly. Or I'm Miranda's top Lieutenant, depending on who you ask."

"Miranda? You mentioned her before." Shepard asked.

"I'm guessing you woke up and someone started guiding you over the comms? That was probably her. She spent two years of her life working on you."

"Hold on. "Shepard held her hand up, "Two _years?_ Were my injuries that bad?"

"I'm no doctor, but it was bad. When you were first brought in here, you were nothing but meat and tubes. Anyone else would've put you in a coffin, but project Lazarus was different. They spent a fortune trying to bring you back. And I guessed it work, judging by the look of things."

"That explains the medical data I've seen. But I still don't get it, what exactly happened that prompted all this?"

"You mean you don't remember?"

"Your ship, the Normandy, was attacked by an unknown vessel out in the Terminus Systems. You ordered a shipwide evacuation, but the pilot, Flight Lieutenant Moreau, tried to stay behind and save the ship. You went to go get him, and managed to get him into an escape shuttle, but before you got in, an explosion blasted you away. You then launched the shuttle, staying behind. That was probably when it happened."

"I remember now, we were searching for geth activity." Shepard disclosed, figuring the man was trustworthy. "When a sensor black spot appeared, and we were attacked."

"Yep, that's basically what happened, from what I hear. But they still haven't found the ones responsible." Jacob said. "Now, do you want to keep playing twenty questions, or do you want to get out of here?"

"I'm ready whenever you are."

"Right. The fastest way to the shuttle bay should be-"

 _"Check. Check."_ A male voice interrupted from Jacob. _"Anybody on this frequency? Is anyone still out there? Hello?"_

"Wilson, that you?" Jacob responded. "This is Jacob. I'm here with Shepard. We just took out a few mechs over in D Wing."

 _"Shepard's alive? In in the-... Nevermind. You both need to get out of there. Go through the service tunnels and get to the network control room."_

"Roger, Wilson. Stay on this frequency." Jacob responded.

"Let's go." Shepard said.

"Right. We can access the service tunnels through that door."

Shepard nodded, and the two pressed on.

* * *

 _Meanwhile, on Omega_

"Score." A human man commented as he looked at the TARDIS.

"It's a bit of junk." The Batarian commented.

"No, it's a rare antique." The human said. "A genuine Police Box, circa 1963. Do you know how many of these exist? Five. The one on Earl's Court back on Earth, and the ones in various museums in the galaxy."

"It's really not."

"Really now?" The human was condescending.

"Do wooden boxes make sensor black spots every day?" The batarian asked, scanning the TARDIS with his omni tool.

"If that's the case, then we should get this to Aria. You know how much she hates being kept in the dark about things."

"Agreed." The Batarian said. The Batarian motioned for a few Krogan to come over, and ordered them to lift up the TARDIS.

The Krogan carried the TARDIS away, leaving nothing but a vacant alley.

* * *

"Damn it, Wilson!" Jacob cursed as he and Shepard entered a room filled with mechs. "Do you mind not putting us on a route straight into enemy territory?"

 _"They are literally everywhere, I'm doing the best I can!"_ Wilson paused for a moment, but spoke up again, voice filled with terror. _"Oh no... They found me, help!"_

"Where are you?" Jacob demanded.

 _"Server room B! Hurry, they're out of control!"_

Shepard and Jacob broke into a sprint, and ran up a set of stairs, into the server room.

"I'm hit! They shot me!" Wilson said, a few smoking mechs on the floor, as the two entered the server room.

Shepard, thinking quickly, went over to the first aid station, and administered medi gel.

"Thanks." Wilson grunted as he got up. "Never thought you'd save my life, Shepard. Guess that makes us even now." Wilson leaned on a container, to take the pressure off his leg. "Thought if I came here I'd be able to shut down the mechs. But whoever did this completely fried the system, made it completely irreversible."

"Damn." Jacob cursed. "Any idea who it was? If we can find 'em, maybe we can get them to stop the mechs. We should find Miranda, maybe she has an idea of who it was."

"Forget about Miranda." Wilson said. "She was in D Wing. The mechs were swarming that area! There's no way she survived."

"She's alive." Jacob said. "She's a lot more tough than that."

"Then why haven't we heard form her, hmm? Face it, she's either dead, or she's the one responsible for all this."

"She wouldn't go through all the trouble to wake me just to waste me." Shepard said.

"Okay then, maybe she's not a traitor." Wilson backpedaled. "But that doesn't change the facts. We're here, she's not. We have to save ourselves. The shuttle bay is only a few-"

Wilson was cut off, by the door on the other end of the room opening, and mechs flooding in.

The three ducked behind cover, but an overload by Wilson on the canisters blocking their path easily took care of the mechs.

"Okay Shepard," Jacob approached, "I've got to level with you here."

"What the hell are you doing?" Wilson demanded.

"The Commander won't make it if she's expecting a stab in the back." Jacob said. "Shepard, the Lazarus Project, it was funded and controlled by Cerberus."

"...What the flying _fuck!?"_


	4. Lazarus Research Station - PART II

"...What the flying _fuck!?"_ Shepard exploded. "Cerberus!? The same Cerberus that slaughtered dozens of innocent people in their experiments!?"

"Shepard, a lot can change in two years." Jacob said. "We're not the same Cerberus you encountered. I don't know how I can prove it, but it's true."

"...Fine." Shepard cooled down. "You haven't given me any reason not to trust you so far. Come on, let's get to the shuttles." Shepard took charge, leading the other two to the shuttle bay.

The door opened, revealing several mechs on the other side. The three instantly opened fire, tearing through the mechs, and successfully making it to the shuttle.

"Come on." Wilson said, as he started to override the door. "We're almost at the-" The door opened, revealing a very pissed off woman on the other side. "Miranda? But you were-"

Miranda pulled the trigger on her pistol, blowing Wilson's head off, and scattering blood everywhere.

"What the hell are you doing?" Jacob demanded, rushing over to Wilson.

"My job." Miranda answered. "Wilson was the one who betrayed us."

"Kinda got the feeling he was looking to shoot me in the back at the first chance." Shepard said, holstering her pistol. "And my feelings are never wrong."

"Good instincts." Miranda complimented. "Some are far too trusting to see that coming."

"So?" Jacob asked. "What do we do now?"

"We get off the station." Miranda said.

"What about the others?" Shepard asked.

"There aren't any." Miranda said. "Us three are the only living things in this entire station."

Shepard sighed. "Then let's go."

"Come on." Miranda guided. The three stepped into the shuttle, and flew away from the station. "Before you meet the Illusive Man, we have to ask a few questions to evaluate your condition."

"Alright." Shepard nodded. She could understand where Miranda was coming from.

Jacob activated his omni-tool, and pulled up Shepard's file. "Okay, says here you were born on Earth, and found abandoned by police in Norway at Dårlig Ulv Stranden. You were then taken back to Canada by an Alliance Captain and your adoptive mother, Hannah Shepard. At eighteen, you enlisted and served on Elysium in the 501st garrison. Later, you almost single-handedly held off an attack by Batarian slavers on the colony. Sound about right?"

"Remember it clear as day." Shepard said. "Never knew who my biological parents were. Only that, for some reason, I wasn't good enough for them."

"I'm sure that wasn't the case." Miranda said. "Okay, let's try something more recent. You had to leave behind a squadmate on Virmire, where you destroyed Saren's cloning facility."

"Gunnery Chief Ashley Williams was KIA." Jacob picked up from Miranda. "You made the call. Why did you leave her behind."

"I had to sacrifice a friend that day, and I didn't do it casually." Shepard said. "Either one of my team died, or Saren's army would've been free to rampage across the galaxy, and she wasn't about to let Kaidan sacrifice himself. If she hadn't... We'd probably all be dead right now."

"Understood, Commander." Jacob didn't press further.

"Shepard, think back to the Citadel." Miranda prompted. "After saving the Destiny Ascension, you nominated someone to be the new human councilor. Who did you choose?"

"Captain Anderson." Shepard stated simply, not hesitating.

"Yes. Captain Anderson is now _Councilor_ Anderson. Though from what I hear he preferred life in the military."

"I can imagine." Shepard chuckled.

"Your memory certainly seems solid." Miranda said. "But there are other tests we really should-"

"Come on, Miranda. Enough with the quizzes." Jacob said. "Shepard's memories are there, and I can vouch for her combat skills personally."

"I suppose you're right." Miranda conceded. "Hopefully, the Illusive Man accepts our little field test as evidence enough."

Shepard nodded, and relaxed, waiting for the shuttle to finally get to where they were going.

* * *

The Doctor, after getting everything that he could from something called a 'public extranet terminal,' started making his way back to the TARDIS, only to realize something.

"What!?" He shouted, channeling his tenth incarnation for a brief moment.

The alleyway that the TARDIS was supposed to be in was completely vacant.

"This is most certainly not good." The Doctor understated. In a bit of a eureka moment, he remembered that all TARDISes, no matter the type or mark, leave residual artron energy where they visit. If the TARDIS was simply picked up and moved, then he should be able to follow the trail by sensing the energy fluctuations with his body alone. Barring that, he could just recalibrate a computer to detect the energy.

Deciding it couldn't hurt, the Time Lord closed his eyes, and smiled once he found exactly what he was looking for. He reopened them, and set off.

* * *

Shepard's shuttle docked, and the three got off. Miranda led Jacob and Shepard into a waiting room, and got to her own work. "The Illusive man is waiting for you in the other room." The Cerberus operative said.

Shepard nodded, and proceeded into the room Miranda pointed to, and walked down the steps, onto a circular platform.

The moment Shepard stepped on, a holographic grid rose up from the circle, surrounding Shepard. The grid flickered, and replaced Shepard's view of the room with a large chamber, with a big window overlooking a dying star. A man was sitting in a simple yet elegant chair in the center of the room.

"Commander Shepard." The Illusive Man greeted, taking a drag from his cigarette.

"Illusive Man. I thought we'd be meeting face to face."

"A necessary precaution." He said, tapping the ash of his cigarette. "Not unusual, for people who know what you and I know."

"And what is that, exactly?"

"Humanity's presence in the galaxy is a lot more fragile than we like to think. And now, we're up against the greatest threat of our brief existence."

"The Reapers."

"Good to see your memory's still intact." TIM smiled. "How are you feeling?"

"Noticed I had some upgrades a few minutes ago." Shepard said. "Hope you didn't replace anything too important."

"No. We needed you as you were when you defeated Saren and the Geth."

"Okay..." Shepard said. "What was it that made you decide to bring me back."

The Illusive Man stood up, and approached Shepard. "We're at war. No one wants to admit it, but humanity is under attack. While you've been sleeping, entire colonies have been disappearing. _Human_ colonies. We believe it's someone working for the Reapers. Just as Saren and the Geth aided Sovereign. You know more about the Reapers than anyone else in the entire galaxy. Cerberus could have trained an entire army with what we spent to train you, but they wouldn't have your knowledge on the Reapers. Training an army ultimately becomes useless when you know literally nothing about the enemy you face."

"If this is a threat to humanity like you say, you need to contact the Alliance and tell them to mobilize."

"They suffered substantial losses fighting Sovereign." TIM explained. "They're rebuliding, and their forces are stretched too thin to waste their resources verifying the Reaper threat. Blaming the abductions on mercs and pirates is easier, and more convenient."

"But Sovereign was trying to harvest _all_ life. Why would the Reapers only attack human colonies?"

"We don't know, not for certain. Perhaps it may be because a _human_ killed Sovereign."

"Okay, say I do believe you and buy that the Reapers are involved. What would you want me to do?"

TIM turned around, and moved to sit in his chair. "I have a shuttle waiting to take you to the most recently attacked colony - Freedom's Progress. Find any clues you can. Who's behind the abductions? Do they have any connection to the Reapers? I brought you back, Shepard. It's up to you to do the rest." TIM tapped a button on his chair, and terminated the commlink.


	5. Freedom's Progress

The Doctor roamed through the sprawling corridors of Omega, stopping once he reached the club, Afterlife. Every one of his Time Lord senses was telling him that the TARDIS was in there, but why?

Deciding that he'd figure out later, he moved over to the club's entrance, attempting to enter before a large alien creature, known as an Elcor, stopped him.

"Stern: Move back, human. You have to wait like everyone else." The Elcor spoke in its monotone.

The Doctor, thinking quick, pulled out his psychic paper, and presented it to the Elcor.

"Apologetically: I had no idea, sir." The Elcor moved aside. "Cordially: Please, enter."

The Doctor bowed, and entered the club. Apparently, the paper looked like a very formal invite to the club from Aria herself (whoever that was).

Shrugging, and storing the paper, the Doctor proceeded long the same trail the TARDIS left. He entered, and saw the iconic shape of the ship in what looked like a VIP area.

He found the TARDIS, but how was he going to get to it?

* * *

The UT-47 Kodiak shuttle sped through the empty vacuum of space, en route to the colony Freedom's Progress.

"We should be there shortly, Shepard." Miranda said. "Orders?"

"Our first priority should be looking for survivors." Shepard said, looking at a datapad. "If someone did survive, then they can tell us what exactly happened."

"It's unlikely there'll be any, Commander." Miranda told the Commander. "No one was left at any of the other colonies. It's likely this one will be the same way."

"It would be nice to fine _somebody._ " Jacob said. "Anything's better than another ghost town."

The shuttle hit the planet's atmosphere, and landed on a small pad on the outskirts of a small mining town.

The team stepped out, and proceeded to look for clues.

"Looks like everyone just got up and left right in the middle of dinner." Jacob commented, a bit unsettled, as they passed through a cafeteria.

"No bodies, no signs of structural damage, or even spent thermal clips." Miranda noted as they passed through a large square. "Whatever happened to them, they didn't put up much of a fight."

Shepard opened a large blast door, revealing a large quantity of mechs on the other side.

"Mechs!" Shepard shouted out, prompting everyone to duck into cover.

"Strange. The security systems were deactivated at the other colonies." Miranda said, as she and the others fought to keep the mechs away.

Shepard took the assault rifle off her back, and started firing at a trio of mechs across the gap.

She succeeded in taking all three out, and moved to aid Miranda and Jacob.

Miranda sent out an overload, causing a mech to explode, with the explosion damaging its surrounding comrades. From there, it was easy to take out the remaining mechs.

"They shouldn't have been hostile." Jacob said as they moved forward. "They should've recognized our IFFs."

"These ones were probably hacked, too." Shepard said. "Contacts." She calmly stated, as two mechs behind a low barrier activated. The two were quickly dispatched, and the three entered the building they were guarding.

Inside was a group of Quarians, looking over a holographic map of the area. The team's entrance caused the Quarians to quickly shoot up from their seats, and ready their weapons, Shepard's team doing the same.

"Prazza!" A younger Quarian got in the way of the Quarians holding their weapons. "You said you'd let me handle this!" The Quarian turned to face Shepard, and stopped dead in her tracks. "Wait... _Shepard?"_

"I'm not taking any chances with Cerberus operatives!" The one in the green suit answered.

"Put those weapons down!" Tali ordered. "Shepard? Is that... you're _alive?_ "

"Yeah, I can hardly believe it myself. One minute, I'm in space suffocating, the next I'm in a medical bay of some kind with a splitting headache. By the way, that geth data I give you help complete your Pilgrimage?"

"Yes... it did." Tali said. "Prazza, weapons down. This is definitely Commander Shepard."

"Why is your old Commander working for Cerberus?" Prazza asked, holstering his assault rifle.

"I don't know." Tali said slowly, looking at Shepard. "Maybe we should ask."

"I got curious." Shepard shrugged. "They spent nearly four billion credits trying to bring me back, so I wanted to see why."

"Likely story." Prazza crossed his arms. "No organization would commit so many resources to bring back one soldier."

"You haven't seen Shepard in action." Tali told Prazza. "Trust me. It was money well spent." Tali then refocused her attention to Shepard. "Perhaps we can work together. We're here looking for a young Quarian named Veetor. He was here on Pilgrimage."

"Why'd he come here?" Shepard innocently wondered.

"Quarians get to choose where they go on Pilgrimage." Tali explained. "Veetor always liked the idea of helping a small settlement. He was always, uh, nervous in crowds."

"She means he was unstable." Prazza piped up. "Combine that with damage to his suit's and an infection from open-air exposure, and he's likely delirious."

"When he saw us landing, he hid in a warehouse on the far side of town. We suspect that he also reprogrammed the mechs to attack anything that moved."

"Veetor's the only one that knew what was going on here." Shepard said. "We should split up, draw enemy fire away from each other."

"Good idea. You'll need two teams to get past the drones."

"Now we're working with Cerberus?" Prazza asked, a bit incredulous at the mere suggestion of the idea.

"No, Prazza, you're working for me." Tali got stern. "If you can't follow orders, go wait on the ship." She told him, then turned to Shepard. "Head for the warehouse on the far side of town. We'll circle around the far side and draw off some of the drones to clear you a path."

"Sounds like a plan." Shepard nodded in agreement. "Make sure to stay in radio contact."

"Will do." Tali responded. "Good luck, Shepard. Oh, and by the way... it's good to see you again."

"You too." Shepard responded.

The Quarians went first, heading out the door on the far end of the room, leaving Shepard to take the door on the left. Three hovering security drones whizzed past, flying up ahead to cut off Shepard's team. The team moved through more buildings, stopping at a large outdoor pavilion, where the drones had set down. The team dove into cover, getting out of the drones' sights.

Fortunately, they weren't that tough to deal with. The drones had the ability to fly quite easily, but to do so meant sacrificing even the most basic armor plating. To make up for it, they had shields, but they were quite weak, which meant that a few well-placed overloads cracked the drones wide-open.

 _"Shepard!"_ Tali radioed. _"Prazza and his squad rushed on ahead. I told them to wait, but they wouldn't listen! They want to find Veetor and take him away before you get here!"_

"Come on, we can still catch up to them." Shepard led the other two through more buildings, eventually coming to a large quarry-like area, with another blast door set into the rock. More drones flew down from the air, being taken out by a few overloads and well-timed shots. After the last of the drones were destroyed, Shepard ordered Jacob and Miranda on the side of each door, Shepard ducking down behind a barrier directly in front of the door.

The door then opened, revealing a grizzly sight.

A large mechanized behemoth, the YMIR mech, was mowing down Prazza's squad, quite literally crushing one of them. Tali, fortunately, seemed unharmed, but it wouldn't remain that way for long if Shepard didn't take care of it.

Shepard's squad rushed in, ducking behind more crates.

"That mech's got heavy armor plating!" Jacob shouted out. "It's gonna take some really big guns to crack it!"

Miranda fired a high-powered overload at the mech, taking out its shields, but at the expense of having a greatly increased recharge time.

Shepard, thinking fast, got the grenade launcher she still had from the Lazarus Research station. It unfolded, and the Commander found herself taking aim at the walking giant.

Two shots from the grenade launcher were able to damage its armor enough to allow normal weapons to finish it off, but doing so was no small task.

The moment Shepard or one of her teammates popped up from cover, the YMIR would react with lightning-fast reflexes, shooting at them.

Which meant that getting a shot clear enough would be nearly impossible.

But like all mass effect based weaponry, the mech needed to vent the built-up heat in order to prevent damage. If one of them could get a shot on the mech in just the right place while it was doing so then it wouldn't be able to vent said heat.

"Miranda!" Shepard shouted out. "I'm going to distract it, once it starts venting, you take the shot!"

Miranda nodded in compliance, and Shepard sprinted out of cover, making sure to keep within the mech's sights.

The large automaton slowly pivoted around, firing it's machine gun as it turned. The mech stopped firing, and two small panels on its back opened, allowing the heat to vent out.

Miranda, seeing her opportunity, fired into one of the vents, the shot damaging the mechanism that opened the vents. The vents closed, and a large crack came from the mech, signaling that the vents' opening mechanism had been broken. The mech, after continuously firing for a few more moments, stopped. It tried to vent the built up heat, but couldn't, making it impossible to fire its weapons.

The team, seeing their chance, popped out of their cover, and focused all of their fire on the mech, causing it to explode in a blaze of glory.

"Nice work." Shepard complimented. "Let's get to Veetor, find out what happened, and get out of here." She said, entering the warehouse.

Inside, a Quarian was sat in front of a large array of monitors. "Monsters coming back." The Quarian rambled frantically. "Mechs will protect. Safe from swarms. Have to hide. No monsters. No swarms. No-no-no-no-no."

"Veetor?" Shepard addressed.

"No Veetor. Not here. Swarms can't find. Monsters coming. Have to hide." The Quarian continued to ramble.

"Relax, Veetor. There aren't any monsters here." Shepard tried to calm him down, but he just kept rambling.

"I don't think he can hear you, Commander." Jacob said, looking down at the frantic alien.

In response, Shepard activated her omni tool, tapping a few controls on it. She waved it in the air, causing the screens to crash and deactivate.

Veetor leaned back from the keyboard, and got up, turning around to face Shepard. "You're human." Veetor noted in amazement. "Where did you hide? Why didn't they find you?"

"We're not survivors, Veetor." Shepard gently explained. "We only just got here."

"You don't know." Veetor said, turning back to the screens. "You didn't see. But I see everything." Veetor entered a few commands, and surveillance video of the colony started playing.

On the screen, cockroach-like humanoids were carting off pods of some kind, while swarms of what looked like bugs clouded the screen.

"What the hell is that?" Jacob asked, looking at the alien.

"I think..." Miranda looked amazed and surprised. "I think it's a Collector."

"A what?"

"A Collector. We don't know much about them, they usually work through intermediaries, like slavers or hired mercenaries. If they're involved with the Reapers somehow, it could explain what happened to the Colonies."

"What I want to know is _how_ they keep taking whole colonies." Shepard said.

"From the small samples we've got from them, the Collectors have technology light-years ahead of ours. They could have something that disables a whole settlement at once." Jacob hypothesized.

"The seeker swarms." Veetor told them. "Tiny machines, like insects. The seekers find you. Freeze you. Then the monsters take you away."

"Freeze?" Miranda repeated. "Sounds like the seekers hit their victims with some kind of stasis field or nerve toxin."

"How'd you avoid being frozen?" Shepard asked the Quarian.

"Swarms didn't find me. Monsters didn't know I was here." Veetor explained.

"Sounds like either his suit protected him, or they weren't seeking out non-human life-signs." Jacob theorized.

"What happened after the seekers froze everyone?" Shepard asked.

"The monsters took the people onto the ship, and then they left." Veetor explained quickly. "The ship flew away. But they'll be back for me. No one escapes!"

"I think that's all we're going to get out of him, Commander." Jacob said.

"Thank you, Veetor." Shepard remained polite. "You were very helpful."

"I studied them." Veetor told Shepard. "The monsters. The swarms. I recorded them with my omni tool. Lots of readings. Electro-magnetic. Dark energy."

"We need to get this data to the Illusive Man." Miranda said. "Grab the Quarian, and-"

"What?" Tali interrupted, walking in. "No! Veetor needs a doctor, not an interrogator!"

"We won't hurt him." Jacob said. "We'll bring him back after he gives us what we need."

"Veetor goes with Tali, end of story." Shepard said.

"Thank you, Shepard. I'm glad you're the one still giving the orders." Tali nearly hugged the Commander. She took her own omni-tool, and sent something to Shepard's. "Here's all of Veetor's omni-tool data. Think of it as a thank you present. I've got to go, but it was good seeing you again. Good luck out there, Shepard." She said, as she left the warehouse, and went back to her ship.

* * *

The holocommunicator activated, and Shepard was once again transported to the Illusive Man's office.

"Shepard. Good work on Freedom's Progress." He complimented. "The Quarians have sent forward their findings from Veetor's debriefing. No new data, but it's a surprising olive branch, given our history. You and I have different methods, but I can't argue with the results."

"It pays to have actual friends every once in a while."

"Diplomacy is great when it works, but difficult when everyone already perceives you as a threat. But more importantly, you confirmed the Collectors are behind the abductions."

"Somehow, I get the feeling that you already knew." Shepard said.

"I had my suspicions, but I needed proof. The Collectors are enigmatic at best. They periodically travel to the Terminus Systems, looking to gather seemingly important items or specimens. Usually in exchange for their technology. When their transactions are complete, they disappear as quickly as they arrived, back beyond the unmapped Omega 4 relay. Until now, we've had no direct evidence of their aggression."

"Why's the Omega 4 relay unmapped? What do we know about it?"

"Only that no ship passing through it has ever returned. Our best guess is that the relay somehow reacts differently to Collector vessels, allowing them safe passage. If they can manipulate relays like that, then that's only more evidence of a connection to the Reapers."

"Any ideas on why they're targeting humans?"

"If the Collectors are agents for the Reapers, it could be any number of reasons. Humanity played a key role in destroying Sovereign. That might have been enough to get their attention. Why really concerns me is why the bother abducting the colonists. If they're paralyzed, why not just kill them?"

"You said before that the Collectors have taken people before. What do they get from those kinds of deals?"

"The Collectors aren't very forthcoming about their motives. Generally, they seek out species with rare genetic mutations or abnormalities. A dozen two-hearted humans, for instance. They pay slavers or merc groups exorbitant sums to obtain these specimens. And then they leave. But they've never targeted one single species before. And the previous samples were in the dozens, not the tens of thousands."

"But how do we know there's a connection to the Reapers?"

"The Collectors only started targeting humans after the destruction of Sovereign by you and the fifth fleet. The abductions _are_ related, even if the Council and the Alliance refuse to believe it. I'm not going to wait while the Reapers are on the march. We need to take the fight to them."

"If I'm doing that, I'll need an army. Or a really good team."

"I've already complied a list of soldiers, scientists, and mercenaries." He said, as a smaller holoscreen activated next to his chair. "You'll get dossiers on the best of them. Finding them and convincing them to work with you could be challenging, but you're a natural leader. I'll continue to track the Collectors. When they make their next appearance, I'll notify you and your team. Be ready."

"Done." Shepard said. "Just so you know, this does not make me part of Cerberus. If you do one thing that I don't like, this partnership is over."

"I wouldn't expect anything else." The Illusive Man took a drag from his cigarette. "Twothings before you go: First, head to Omega and find Mordin Solus. He's a brilliant Salarian scientist. Our intelligence suggests that he may be able to find a way to counteract the seeker swarms. We've also detected a sensor anomaly on the station, identical to the black spot recorded by the Normandy before its destruction. There's no concrete evidence on whether or not it's connected to the Collectors, but it won't hurt to know more about it."

"Sounds good. The other thing?"

"I found a pilot I think you might like. I hear he's one of the best. Someone you can trust." The Illusiva Man finished, and the link cut.

"Hey, Commander." Someone greeted as they entered. Shepard turned around to face the man.

Joker smiled. "Just like old times, huh?"


	6. Omega

_I've often been told that miracles don't exist. That they're nothing more than mere coincidences, which we use to give meaning to our lives._

 _The opposite is true. Miracles_ do _exist. They happen every day, in little ways. But sometimes, they happen in big ways. Ways that can change life forever._

 _And there was no bigger miracle than the Doctor meeting the Shepard. Nowadays, we all know the tale of the mysterious medicine man who appeared from nowhere, and helped Shepard defeat the Reapers, but back then, no one knew anything about him. Where he came from, who he really was, why he was there._

 _And the act of trust on Shepard's part was simply... astonishing. The Commander was slow to trust. Not trust in the sense of simple things like paying you back when you give them money, or trusting that they'll take your shift at work for you._

 _No, real trust. The trust that you can give someone your deepest, darkest secrets. The trust that you can let them in on your emotions, and they won't take advantage of you. That's the kind of trust that Shepard gave the Doctor._

 _She let an unknown, practically a loose cannon on board her ship, allowing him to roam freely, and let him help._

 _You see,_ that _is a miracle. Willing to trust a man you have literally no information on._

 _And without that miracle, we may not have defeated the Reapers._

-Introduction to Chapter 2, A Completely Accurate Account of the Shepard by Professor River Song.

* * *

"I can't believe it's you, Joker." Shepard said, as the two walked through the corridors of Minuteman Station.

"Look who's talking, I saw you get _spaced._ " Joker responded.

"I got lucky. With a _lot_ of strings attached. How'd you get here?"

"It all fell apart without you, Commander. Everything you stirred up, the Council just wanted it gone. Team was broken up, records sealed, and I was grounded. The Alliance took away the one thing that mattered to me, hell yeah I joined Cerberus."

"You really trust the Illusive Man?" Shepard asked, as the two stopped in front of a large window, overlooking a silhouette of a starship.

"I don't trust anyone who makes more than I do. But they saved your life, let me fly... And then there's this." Joker said, as lights started illuminating the ship. "They only told me last night."

Each one of the lights reflected off a shiny metal hull, showing off an almost identical recreation of the Normandy, albeit painted in Cerberus colors.

As the light glistened off the hull, Shepard thought she would cry.

"It's good to be home, huh Commander?" Joker said, looking over the replica.

"I guess we'll have to give her a name."

There was only one choice in that regard.

* * *

Shepard exited the Normandy's airlock, and started to walk down the corridor linking the bridge to the CIC. Several workstations lined the walkway, with the crewmembers at their posts.

Shepard stopped at the top of the stairs, and looked over the CIC. Finally, it felt like she was really, properly back.

"Welcome aboard the new Normandy, Commander." Jacob said.

Shepard walked down the stairs, and stopped in front of the Normandy hologram.

"I've been looking over the dossiers." Miranda said. "I strongly recommend starting with Mordin Solus, the Salarian scientist on Omega. He's quite possibly the only one that can provide us with a countermeasure for the seeker swarms."

"And without that countermeasure, we'll be helpless if the Collectors decide to attack us."

"I'll tell Mr Moreau to set a course for Omega immediately, Commander." A voice rang from overhead.

"Who are you?" Shepard asked. Behind her, a blue hologram, resembling a pawn, was projected over one of the terminals.

"I am the Normandy's artificial intelligence. The crew like to refer to me as EDI."

"Helmsmen aren't happy when someone takes control of the ship away from them." Shepard shook her head. "Especially Joker."

"I do not helm the ship." EDI explained. "Mr Moreau's talents will not go to waste. During combat, I operate the electronic warfare and cyberwarfare suites. Beyond that, I cannot interface with the ship's systems. I observe and offer analysis and advice, nothing more." She said, disappearing.

"Right, since EDI's already taken care of the course setting part, I'll be in my quarters. Somehow, even though I've been dead for two years, I feel like I haven't slept in days."

"Got it, Commander. I'll let you know when we arrive." Miranda said.

Shepard nodded, and went up to her quarters, intent on getting some shut-eye.

Then, all of a sudden, a man (probably one of the crew) rushed up to her, and took off his bowtie. "See? Like so." Then, he ran off.

Shepard just shrugged, and continued.

* * *

 _Several hours later_

The Normandy zipped through space, approaching the mushroom-shaped space station known as Omega. The ship maneuvered into a docking cradle, and the docking tube attached to the Normandy's airlock.

Shepard, Miranda, and Jacob disembarked.

"This place is disgusting." Shepard vocalized her present disgust, looking at the scenery.

"Ah! Welcome to Omega!" A Salarian greeted them. "You're new, aren't you? I can always tell. Allow me to-"

"Leave, Fargut." A batarian ordered, coming up from behind the Salarian. "Now."

"Of-of course, Moklan! Whatever she wants!" The Salarian then promptly ran away.

"Blasted scavengers. Welcome to Omega... Shepard."

"You know who I am?"

"Of course." The batarian got condescending. "We had you tagged the moment you entered the terminus systems. You're not as subtle as you think. Aria wants to know what brings a dead Spectre to Omega. I suggest you go to Afterlife now and present yourself."

"I'll go to afterlife when I damn well please. Now get lost." She drew her pistol.

The batarian shook his head, and walked away.

"I'm receiving quarantine warnings in the slums where Doctor Solus runs the clinic. Anticipate resistance at the transport station. I have also accessed messages between mercenary groups regarding plans to deal with Archangel. There is a recruiter in Afterlife that may have more information. The sensor black spot identical to the one detected by the original Normandy is also inside the club."

"So, Afterlife it is." Shepard said, continuing forth. As she got closer to the exit of the docking bay, Shepard noticed somebody beating up a batarian pretty badly. Remembering an E-Mail that the Illusive Man had sent her, she approached. "You Zaeed Massani?"

The man turned around, revealing his worn, heavily scarred face. "Yeah. That's me. You must be Commander Shepard. I hear we have a galaxy to save."

"Welcome aboard, Zaeed. Get your gear, and get aboard." She then looked down at the injured batarian. "After you deal with him, of course."

"Of course. I assume the Illusive Man told you about our arrangement?"

"Not really, no."

"Hmm, good thing I decided to ask, then. Picked up a mission a while back, before I signed on with Cerberus. Thought you might be interested. You heard the name Vido Santiago? He's the head of the Blue Suns, runs the whole damn organization. Seems he recently captured an Edfell-Ashland refinery on Zorya, and is using the workers for slave labor. The company wants it dealt with."

"I think we have time to do that."

"Good. Get it out of the way so we can focus on being big goddamn heroes."

The batarian behind them suddenly shot up, and started printing to the end of the hall. Zaeed just took his pistol, and shot the batarian in the leg. "I better turn this thing in before it starts to stink." He said, picking up the alien. "I'll be locked and loaded the next time you're ready to get some killing done." With that, he walked off.

Shepard and co followed suit, and left the docking bay, and entered Omega proper.

Thumping music came from the large building marked 'Afterlife.' Several people were lined up to enter, members of the various species among them.

The large doors opened, and the three stepped inside, into a long corridor. As the team went along, a group of three batarians suddenly got in the way.

"What're you looking at?" The batarian growled.

Shepard was fast to draw her pistol. "The man who's day I'm about to ruin."

"Uh... I'm not looking for trouble." The batarian stammered.

"Maybe _I_ am." Shepard retaliated. "Maybe you'd better get out of here before I find you some."

"Alright, alright." The batarian quivered. "I've got stuff to do anyway." The batarian turned to his comrades. "Come on. Let's get out of here."

One of the batarians, however, didn't let it go. He tilted his head, and made a cutting motion at his throat.

Shepard just shot him right in the thighs. "Next one's going somewhere a _lot_ more uncomfortable."

The batarian just limped off in fear.

"You... really don't like batarians, do you?" Miranda commented.

"No... Not really."

The three walked through another large door, and entered the club. Music and the sounds of partying filled their ears, as the three walked around the club. Shepard, spotting a strangely dressed man looking very uncomfortable. The man seemed... off, somehow. Curious, Shepard approached.

"Not your kind of place, is it?" She asked the stranger.

"No... I'm used to a bit more... pizazz at my parties." The stranger looked around in discomfort. "And the dancers creep me out. They're _too_ flexible."

"Then why are you here?"

"...Someone took something of mine." The stranger admitted, after a moment of silent thinking. "See that box up there?"

"The one marked 'Police?'"

"Yeah. I went off for five minutes, and when I come back..." The stranger made a sort of explosion sign with his hands. "I had assumed it dematerialized, but I didn't hear the engines going..."

Shepard thought the man was crazy, who wouldn't? But she decided to humor him. "What if I got it back for you?"

"You'd do that?" The stranger was quite obviously surprised.

"Sure. Couldn't hurt. Helping people's what I do." Shepard said. "I'll go get that box, and be back before you know it." Leaving the man to his own devices, Shepard walked away.

"Commander, while you two were talking I took the time to scan the box." Miranda began. " _It's_ the sensor black spot."

"Okay, strange man asking us to get the box which also happens to be the sensor black spot the Normandy recorded. That's most definitely not a coincidence. When we get back to him, we're asking that man just what the hell is going on." Shepard led the team up the stairs, past the guards, and up to Aria.

"That's close enough." Aria ordered, looking over the club.

The three stopped in their tracks as Aria's goons started pointing weapons. One of the guards holstered his pistol, and started scanning Shepard, the scan coming up negative.

"If you're trying to scan for weapons, you're doing a really shitty job." Shepard remarked.

"Can't be too careful with dead spectres." Aria said. "Could be anyone wearing your face."

"She's clean." The batarian doing the scanning said.

"You're the one who runs Omega?" Shepard asked as she approached.

Aria laughed. "I _am_ Omega. But you need more. Everyone needs more something. And they all come to me. I'm the boss, CEO, Queen if you're feeling dramatic. It doesn't matter. Omega has no titled ruler and only _one_ rule." Aria sat down. "Don't _fuck_ with Aria." The Asari smiled.

"Sounds like me and you have similar rules." Shepard commented.

Aria just offered Shepard a seat.

"So, what can I do for you?" Aria asked.

"I'm looking for somebody called 'Archangel.'"

"Archangel?" Aria's eyebrow-shaped tattoos rose. "You want him dead too?"

"No. I want him to join me on my team."

"Interesting. You are going to make some enemies teaming up with Archangel. That's assuming you van get to him. He's in a _lot_ of trouble right now."

"What kind of trouble?"

"The local merc groups have joined forces to take him down. They've got him cornered, but it sounds like they're having trouble finishing him off. They started hiring _anyone_ with a gun to help."

"That's probably our ticket in." Jacob commented.

"They've set up a recruiting station just over there. I'm sure they'll let you in."

"I'm also looking for Mordin Solus. You know where I can find him?"

"The salarian doctor? Last I heard he was trying to help plague victims in the quarantine zone. I always liked Mordin. He was always as likely to heal you as he was to shoot you."

"Where is he?"

"The Gozu district slums. There's a transport station over in the markets. Anything else?"

"Yeah. I talked to the man who owns that box. He wants it back."

"Take it. It's been nothing but trouble."

Shepard was curious. "How?"

"Two of my men broke every bone in their arms trying to force those doors open. Then, another one got his leg chopped off while trying to cut through it with blade saw. After that, a Krogan got hospitalized while trying to headbutt it open. At this point, I just want it gone. Hell, I'll even roll out the red carpet."

"Okay, glad that's settled." Shepard got up. "Thanks for the info."

"Yeah. Just make sure that box is out of my sight within fifteen minutes, and we won't have any problems."

Shepard walked back down the stairs, and to the stranger. "I got your box back for you."

"Oh, really?" The stranger look excited. "Thanks... whoever you are."

"Don't mention it. You know, I don't think I got your name either."

"It's the Doctor."

"Doctor? Doctor Who?"

"Ooh, dangerous question."

"Yeah? Well you'll find that I quite like danger." Shepard smiled. "So, that box of yours... what is it?"

"I suppose a little looksie couldn't hurt." The Doctor shrugged. "But your, ah, friends will have to stay outside. 'S a bit cramped." He said, as they walked up the stairs to the TARDIS. "You ready?" He unlocked the doors, and pushed the right one in. Shepard entered first, and the Doctor followed close behind, shutting the door before anyone else could see inside.

"Oh. My. _God!_ " Shepard yelled, her voice echoing off the walls. "It's... it's... it's..."

"Aren't you going to say it's bigger on the inside?" The Doctor prompted.

"That's quite obvious, isn't it?" Shepard looked around the console room. "What is it? What does it do?"

"'It' is called the TARDIS. That stands for Time And Relative Dimension In Space. And it's a ship."

"Wait a minute, time?" Shepard realized. "Surely that doesn't mean it..."

"Travels in time? Of course it does."

"How would you even do something like that?" Shepard asked.

The Doctor held up his finger in a 'hold that thought' gesture, and started setting the controls. He hit the dematerialization lever, and the engines engaged. A moment later, they stopped again. He motioned for Shepard to wait, and he stepped outside.

A moment later, he came back in, his bowtie missing from around his neck.

"That was you!" Shepard realized. "Oh my god, I'm in a _real_ time machine!" Then, and idea popped into her head. "Are you from the future?"

"Depends on what you mean." He said, tying his bowtie. "I'm sure I come from _someone's_ future."

"I have so many questions." Shepard said. Then, all of a sudden, something entered her mind, radiating a warm feeling of calmness and serenity. "What's that?"

"What?" The Doctor looked up from setting the controls back for Omega."Oh, that's probably the TARDIS just forming the telepathic link. Funny. It's usually undetectable by humans."

"I guess I'm just a bit more perceptive." Shepard said.

The TARDIS's engines stopped, and the ship materialized on Omega once more.

"Here we are, back on Omega." The Doctor said, guiding Shepard to the door.

"Thank you, Doctor. This was certainly a... unique experience." Shepard said. "Now'll if you'll excuse me, I've got Collectors to stop."

"Collectors?"

"The Collectors. They're the ones responsible behind our colonies disappearing."

"Our?"

"You know, humanity's... Wait, don't tell me you're not human."

The Doctor kept silent.

"You're not human..." Shepard realized. "Two years ago, the population of entire colonies started up and vanishing, and the Collectors are the culprits. I'm trying to stop them."

"Ah, well." The Doctor said. "That is quite a pickle..."

"If you want to help, just say so."

"I want to help."

"Ah... Well, I don't know where you'll be most effective. But we could at least use another capable pair of hands right now." Shepard said. "I'll send word to the Normandy, let them know that you're coming aboard. See you on the ship, Doc." She then left the TARDIS.

After Shepard was gone, the TARDIS spoke up. _'You felt it too, didn't you?'_

"Yeah. I did." The Doctor said. "But it's not possible."

 _'We_ are _in another universe. Anything's possible.'_

"I suppose it is. You think she knows?"

 _'I don't think so.'_

"Then let's see if we can't try to keep it that way."


	7. Omega: The Professor

**_Merry Christmas!_**

* * *

 _Normandy briefing room_

"Wait, you just _let_ him on the ship!?" Miranda demanded.

"Relax, Miranda." Shepard tried to calm the Cerberus opoperative down. "He's good."

"Oh, really!? _A complete unknown_ is safe to let on board the ship!? You should have cleared this with me first."

Shepard frowned. "In case you forgot, it's _my_ ship, not yours. I'll let on board who I damn well please."

"I get that, Shepard, but we know nothing about him. Who he is, where he's from, or what his motives are. And you let him on board without a second thought."

"Miranda, right now my hunch is telling me that that man is someone we want to have on our side. And my hunches have never been wrong."

"If there's one thing I've learned with twenty years of merc work, is to always follow your gut." Zaeed interjected.

"See? Zaeed agrees with me."

"Because he's been paid to."

"Okay, if you won't accept my hunch as him being good enough, I'll simply say this. The things I saw... He couldn't fake them, not in the slightest." Shepard said. "For the moment, he's worthy of a little modicum of trust."

"Shepard, you still haven't told any of us what you saw in the box."

"And I don't intend to. Everyone has secrets, and that one's his to tell. Now, I believe we have a Professor to recruit." Shepard said.

"Is your new friend coming along?" Miranda asked sarcastically.

"Yeah, why not? I need to see how he does in the field, and there's no better way to test that than bringing him along. Myself, Jacob, Zaeed, and the Doctor will get suited up. You'll have command of the Normandy until we get back."

"Understood, Commander."

* * *

"...That can't be right." The Doctor said, looking at the screen. "Run it again."

 _'I've run the test three hundred times, even though it wasn't necessary to begin with. Face it, my thief, all we felt was a little ghosting.'_

"...Yes, I suppose you're right." The Doctor pushed the monitor away, when a knock came from the door. The Doctor rushed to answer it, seeing one of Shepard's crew outside, the Cerberus officer. "Ah! Yes! Hello!" The Doctor vigorously shook her hand, shutting the door behind him. "I'm the Doctor." He said, releasing her hand.

"Yes, quite right." Miranda looked a bit put off by the Time Lord's enthusiasm. "The Commander's going on a mission, and she wants you to go along as well. Head up to the armor and get a suit-"

"Don't need it."

"-and a few weapons."

"Don't need them." The Doctor said.

"There's going to be a lot of shooting in all likelihood."

The Doctor shrugged. "Never stopped me before." He locked the TARDIS, and went over to the Normandy's elevator. He stepped inside, and went up a few decks.

Miranda blinked, not expecting the encounter to go anything like this. Granted, it could've gone a lot worse, but...

She was in the cargo bay, alone, with the Doctor's mysterious box.

Anything could happen.

* * *

The Doctor walked through the CIC, and stepped into the airlock, where Shepard and her team were waiting.

"Didn't I tell Miranda to get you some weapons and armor?" Shepard rhetorically asked, already knowing the answer.

"Don't need them." Okay, maybe she didn't already know the answer.

"Doctor, there's more than likely going to be shooting. Without a weapon and armor, what're you going to do to defend yourself?"

"I don't need a weapon to defend myself. Not when I have this." The Doctor produced a wand-like apparatus from his inner coat pocket.

"And what's that."

"A sonic screwdriver."

"Yeah, and I bet you have a laser spanner, too." Zaeed chuckled.

"I did, but Emily Pankhurst stole it from me." The Doctor explained completely seriously.

"And what's a 'Sonic Screwdriver' going to do against this?" Shepard asked, holding up her gun.

The Doctor remained silent, instead opting to just show Shepard. He flicked the screwdriver open, and pointed it at Shepard, pressing the button. The Doctor then took the gun from Shepard, looking at it in disgust as he did so, but still took it.

He pointed it at the wall, pulled the trigger, and nothing happened.

He used the screwdriver on the gun again, and handed it back to Shepard.

"Okay, that's actually kind of useful." Shepard admitted. "Just don't use it on any of us." The airlock opened, and the four left the ship.

* * *

The four approached a Turian guarding a door with a holographic overlay.

"I told you to get lost, lady!" The turian argued with a human woman. "The plague has the whole zone quarantined! Nobody gets in!"

"I'm human you ass!" The woman shouted back. "Humans can't get the plague! Now let me in before someone takes my stuff!"

"This thing affects every other race out there! We're not taking chances. Nobody gets in until the plague has run its course." The turian said.

"There's a salarian named Mordin Solus in there." Shepard said to the guard. "I've got to go in there and find him."

"The doctor? Crazy bastard opened up a clinic in the district a few months back. The Blue Suns weren't too happy when he moved in. I hear he's trying to deal with the plague. I wish him luck, but the area's still locked down. Our orders are to wait until either the plague or the Blue Suns kill everyone, then go in and clean up."

"Look, do we look like looters to you?" Shepard asked, pointing at herself and her charges. "If I find any looters or Blue Suns, I'll kill them. Anyone gets in my way, I'll kill them too."

"Okay, you think you can fix this, why not? I'll radio ahead, let them know you're coming."

"Wait, you're stopping me but not them?" The human from earlier asked. "You son of a bitch!"

"You don't have a grenade launcher lady." The turian responded. "Now get lost."

Shepard, meanwhile, walked back over to her group.

"Fortunately enough for us, humans are immune." Jacob pointed out.

"Fortunately for most of us." The Doctor corrected. "I should still be fine, though. Us Time Lords, we tend to be immune to most forms of disease."

"You sure?" Shepard wanted to make sure.

"Positive." The Doctor nodded. "Unless it's been specifically designed to attack a Time Lord's immune system, I'll be right as rain. Oh, forget that last bit, that was rubbish."

Shepard just shook her head, and led the three through the airlock into the quarantine zone. Once they stepped through, all of them that had weapons readied them, and prepared to fight.

"Don't shoot, they're clear to come in." One of the guards said to the others as Shepard's team approached the checkpoint.

"'Gozu District'" The Doctor read from one of the signs as they passed. "Sounds a bit too much like 'Gozer' for my tastes... You know, that kind of reminds me of the time I met an Elder God..."

Shepard ignored him, instead leading the three into the district proper. She spotted two Blue Suns in front of a door, and readied her sniper rifle. She took aim at one of their heads, and opened fire, blowing off his head. The other one was also easily dealt with.

"You okay?" Shepard looked over at the Doctor, who looked _very_ disgusted.

"Yeah, it's just... Leaving the dead in the streets like this?"

"It looks like they were burning them. Trying to keep the plague from spreading." Jacob said.

"That still doesn't exclude common courtesy." The Doctor said.

"Come on." Shepard ordered. "We can argue ethics later."

The team moved forward, but Shepard stopped when they came across a batarian sitting on the floor, writhing in pain.

Shepard approached, and crouched down to eye level.

"Human." The sick batarian spat. "Should have guessed." He coughed. "Bad enough you infect us with this plague. Now you lack the decency to even wait until I die before you come to steal my possessions."

"We're not here to rob you." Shepard said. "We're here to help. Is there anything we can do?"

"Get away, human!" The batarian suddenly shouted, leveling a weapon. "Your kind has done too much already! Your plague did this to me. Your feigned pity is the final insult."

"Fine, be that way. I'm here to find Mordin Solus, you know where he is?"

"Humans looking for the human sympathizer. I hope the Vorcha burn he and his clinic to the ground." The batarian started to get worse. "I hope you... I hope..." The batarian started hacking.

Shepard sighed, and activated her omni-tool, applying medi-gel to the batarian. "This probably won't cure it, but it'll help."

The batarian looked amazed. "You... you helped me. Why?"

"Everyone, no matter what they've done, deserve at least a little kindness." Shepard said. "I don't like batarians, but they're also on that list. Now, I'm going to go cure this plague, but to do that I need to find Mordin. Where is he?"

"Your words sound... sincere. Maybe it's the fever, but... what do I have to lose? His clinic is on the far side of the district, near the environmental control fans. The route there's swarmed with Blue Suns and Vorcha, but you look like you can handle them. But be careful with Mordin, he's... dangerous."

"How so?" Shepard wondered.

"The Blue Suns tried to press him for protection money. He stunned them with some kind of nerve toxin, then gunned them down. He's not just a doctor. Doctors don't execute people and display the bodies as a warning."

The Doctor shivered at that last part.

"Right, we've got to go now, but I'll send someone back to help you." Shepard told the batarian.

"Goodbye, human. Thank you."

The four proceeded, but the Doctor started coughing, worse than a cigarette smoker. "Oh, that's not good."

"Doctor?"

The Doctor proceeded to scan himself with the sonic screwdriver. "Yep, I've definitely got it." He said, looking at the readout. "Highly degenerative respiratory disease-that's what the plague is. I don't have lungs like humans and the other species, so it'll take a little while longer to effect me."

"You're one crazy nut, you know that?" Zaeed said.

Shepard just ignored him. "How long?"

The Doctor took a moment to answer. "A few hours. Probably. But no more than two. Or one. Maybe half. I think I'll stop talking now."

"If we get to Mordin's, can you cure it?" Shepard asked.

"If he has the supplies, yes." The Doctor coughed again. "Ow."

Shepard nodded her acknowledgment, and led the team forward, the team(excluding the Doctor) killing the Blue Suns they came across along the way. As they got to a large plaza, they noticed a firefight in full swing, between the Vorcha and Blue Suns.

Deciding to let half of the problem take care of itself, she watched as the Blue Suns ruthlessly gunned down the Vorcha and their Varren.

After the vicious aliens were killed, the team popped out of cover, and mowed down the remaining Blue Suns.

"Doctor, how you doing?" Shepard asked the Time Lord.

"Feeling fine! *cough* Okay, a bit clammy. *hack* Fine, my respiratory system feels like it's on fire!"

"Don't worry, Doc." Zaeed pointed to a sign. "We're here."

"We got a plague victim coming through!" Shepard yelled to the guards, who opened the door in response. The four entered the clinic, walking to the back area.

"...malanarin." Shepard heard Mordin say to one of the nurses as she approached. "Plenty on hand. Almost as good. Causes cramping in batarians. Supplement with butemerol."

The Doctor coughed, catching Mordin's attention. The Salarian dropped what he was doing, and approached the Time Lord.

"Hmm, curious." Mordin scanned the Doctor with his omni-tool. "External appearance identical to human, internal physiology however... Hmm, doesn't seem to posses lungs in traditional sense. Pulmonary tubes, parallel to lymphatic system. Will take a moment to formulate treatment."

"Mordin Solus?" Shepard asked the salarian, who was at work getting something whipped up to help the Doctor. "I'm Commander Shepard. I'm on a mission, and I need your help."

"Mission? What mission? No. Too busy. Clinic understaffed. Plague spreading too fast. Who sent you?" Mordin asked, not looking up from his computer.

"Uh, I'm not quite sure how to lay it on you." Shepard admitted, scratching the back of her neck. "Ever hear of an organization named Cerberus?"

That however, did make Mordin look up. "Crossed paths on occasion. Thought they only worked with humans. Why request salarian aid?"

"A race called the Collectors are kidnapping humans from all over the galaxy. We're going to find out why and stop them."

"Collectors?" Mordin scratched his chin. "Interesting. Plague engineered. Collectors one of few groups with technology able to design it. Our goals may be similar. But must stop plague first. Already have cure. Must distribute it at environmental control center. Vorcha guarding it. Need to kill them."

"Great." The Doctor coughed. "More shooting."

"I'll get there and take care of it." Shepard said to Mordin. She then turned to the Doctor. "Doc, I think you're going to have to stay behind."

Overhead, a loud loss of power was heard, and red lights immediately activated.

"What in the hell?" Zaeed asked no one in particular, looking up.

"Vorcha have shut down environmental systems. Trying to kill everyone. Need to get power back on before district suffocates. Here, take plague cure. Also, bonus in good faith. Weapon from dead Blue Suns mercs. May come in handy against Vorcha. One more thing. Daniel, one of my assistants, Went into Vorcha territory. Looking for victims. Hasn't come back."

"We'll find him, Professor."

"Thank you. Told him not to go. But he's smart. Bright future. I hope."

Shepard turned to Jacob and Zaeed. "Come on guys." She ordered, as they sprinted out of the clinic.

The Doctor stayed behind, sitting down on a small cot.

"Interesting internal physiology." Mordin told the Time Lord. "Brain structure highly advanced. Binary vascular system also advanced. Triple-helix DNA, unusual in most species. What species do you belong to?"

"I'm a Time Lord." The Doctor said proudly, then coughed.

"Modified cure complete." Mordin reported, handing a needle over to the Time Lord. "Inject into pulmonary artery equivalent."

The Doctor nodded, and did as told. He perked up upon immediately feeling better. "That was fast."

"Cure designed to be fast acting. No use in curing dead patients." Mordin smiled. "So, mission?"

"I don't know much about it myself. All I know is that humans are going missing, the Collectors are the culprits, and we're trying to stop them. The end result beyond that..."

"Cerberus requesting my involvement concerning. Usually do not reach out to non-humans."

"Yeah, I kind of noticed that while I was probing the ship's databanks. Although, while i was searching around I found something... concerning."

"Concerning how?"

"I think I've been in this universe before."


	8. Interlude I

"Curious." Mordin said, thinking on what he had just heard. "Implying you come from another universe."

"That's right." The Doctor nodded. "I've been to a universe like this one before. Much of Earth's history in this one lines up to what I saw first hand. But I'm not sure it's the same, not yet."

"You have visited alternate universes before?"

"Yeah." The Doctor said. "I've visited one where England was a fascist dictatorship, with me as its leader. Another one where World War II was still being fought in the 1960s. One where the Roman Empire spanned the galaxy. Then there was that time I visited Picard's universe..."

"Picard?" Mordin tilted his head. "From Star Trek?"

"Star Trek? All that's fiction over here? Then again, I suppose there's another universe where all this that's happening right now is nothing but fiction... But the point is, there are all these parallel universes stacked up on top of each other existing at the same time, but never interacting with each other. I got flung into one such universe by accident, we called it 'Pete's World,' long story."

"And you believe you have returned to 'Pete's World.'" Mordin deduced, saying the last two words a bit uncomfortably.

"Yeah, your histories don't line up _exactly._ Like there's no mention of the Cybermen, or Torchwood, but that can all be written off as one of those government conspiracies humans are so fond of. But if this _is_ Pete's World... Then I'm in a lot of trouble, _especially_ if Rose gets wind that I'm here..."

"Rose? An associate of yours?"

"I don't speak badly of my companions, they're all very dear to me, but... She was nice, as is pretty much everyone I travel with, but she was really more of a clingy ex-girlfriend than a companion. She nearly caused a multiversal collapse just trying to get back to me. But hopefully, the walls have strengthened up enough to keep that sort of thing from happening again."

"What is your universe like, Doctor?"

"Well, it's sort of like this one. Except there are a ton more aliens back in mine. Like the Daleks, Sontarans, Zygons, and Time Lords, just to name a select few. Earth gets attacked... a lot. There are also a lot of Eldritch Abominations, as you would call them. Never got that, myself, just because they make you go insane at the mere sight of them doesn't mean they deserve to be called abominations."

As the Doctor finished his miniature rant, the fans overhead activated, distributing the cure. "Ah, that's probably Shepard."

A few minutes later, a young man entered the room.

"Daniel? Okay, not injured?" Mordin checked over his assistant.

"Just a few minor bruises, Mordin, I'll be fine."

Mordin nodded, and walked over to his terminal. "Environmental systems engaged. Airborne viral levels dropping. Patients improving. Vorcha retreating." It was at that moment that Shepard entered the room. "Well done, Shepard. Thank you."

"And thank you from me, as well." Daniel said from the back of the room. "Those batarians would have killed me. For a second there, I thought you were going to shoot them even after they let me go."

"I made a promise. And I _always_ keep my promises." Shepard stated.

"Merciful of you." Mordin noted. "Risky. Would have killed them myself."

"Professor? How could you say that? You're a doctor, you help people!" Daniel shouted.

"Lots of ways to help people." Mordin explained. "Sometimes helping patients. Sometimes executing dangerous people. Either way helps. Go check on the patients." He ordered. "Lots of work to do. Think about what I said." Daniel narrowed his eyes, and left the room. "Good kid. Bit naive. He'll learn. Letting him take over the clinic. Should be able to handle it now that Vorcha are gone."

"We've cured the plague. Are you ready to help with the Collector situation?" Shepard asked.

"Yes." Mordin admitted. "Unexpected to be working with Cerberus. Many surprises. Should finish finish up here. Will not take long. Meet you at your ship. Looking forward to it."

Shepard nodded, leaving Mordin to his business. She then walked over to the Doctor. "How are you holding up?"

"Not bad. Mordin and I talked about a couple things while you were off being a hero."

"You feel up to moving?"

"Sure."

"Then let's get back to the Normandy, get Doctor Chakwas to check you out. Make sure there's no lingering problems."

The Doctor nodded, and pushed himself up off the cot, ready to go back to the ship.

* * *

"Doctor, I'm pleased to say that no traces of the plague remain in your system." Doctor Chakwas said, looking over her datapad. "Your respiratory system is the picture of good health. I can't say the same for the rest of you, however."

"Is there a problem?" The Doctor stiffened.

"I genuinely don't know." Chakwas admitted. "I've never seen a species like yours before. Not even a fully mature Krogan has internal physiology as advanced as yours."

"Why, thank you." The Time Lord beamed, holding a hand over his heart. Or, one of them.

"Well, Doctor, I suppose you're cleared for duty." Chakwas entered something into the datapad. "Just take it slow, however. We don't know the full extent as to the cure's effects on you."

"Oh, please." The Doctor waved off. "Gallifreyan internal physiology is more sturdy than a Nokia." He jumped up. "I'll be fin-" He went to take a step, but fell to the floor. "I'm okay! The right leg just went for a little bit of a catnap, is all. I'm ready when you are, Commander." He saluted. Then he promptly put his hand back down, asking: "Why am I saluting?"

"Look, Doctor." Shepard patted the Time Lord on his shoulders. "You weren't really of much... use, back on that mission. You kept a level head, yes, but you were, how should I put it... kind of just dead weight."

"Oh..." The Doctor's face fell.

"Don't worry, Doctor, it's not anything personal. I just don't want to have to worry about you getting shot."

Oh. The Doctor could definitely understand that.

"For now, I'd like you to work with Mordin on developing the Seeker countermeasure." Shepard directed. "I have a feeling the work will go faster with two scientists rather than one."

The Doctor nodded, and proceeded up to the tech lab.

* * *

 _Meanwhile, a few decks below._

Miranda approached the TARDIS, carrying a set of physical lockpicks.

Miranda got close to the lock, and stuck the picks inside, getting to work.

After about five minutes, she heard a burning noise, and felt the lockpicks vibrate.

She pulled the picks out, only to see the tips of them bubble and melt, molten metal dripping on the floor.

"Must me some kind of security mechanism." Miranda guessed, though she wasn't too sure.

One thing she was sure of, was that she was going to have to break out more heavy-duty tools.

* * *

"Hello Doctor." Mordin greeted as the Time Lord entered the tech lab.

"Heyy..." The Doctor responded. "What're you doing?"

"Formulating seeker countermeasure. Challenging work, though access to proper equipment eases process."

"You know what would really ease the process? Help from a bona-fide Time Lord." He boasted.

Mordin gestured to the lab terminal, and the two set to work.

 _Later..._

"...So then I broke the vases, and the entire planet got sucked into a black hole." The Doctor finished, telling the tale of the time he encountered the creature that claimed it was the Devil.

"No witty one-liners?" Mordin asked.

"No... Should there have been?"

"In your place, would have gladly taken the opportunity." Mordin smiled. "'Go to Hell!' Or something along those lines."

 _Still later..._

"Your universe seems very strange." Mordin commented.

"Yeah... It does give off that impression." The Doctor agreed. "There's a lot of... strange occurrences, especially when time travel gets involved. You know the Greys?"

"Ah. Yes. Inspired by human interactions with salarian pirates. Came to pillage Earth at an early stage of development, but crashed instead."

"Well, in my universe, the Greys were actually their own separate species. They were a cloned save race, but who made them was a pretty big mystery on Gallifrey for the longest time. Their masters just up and disappeared one day, and the Greys were left behind, no more intelligent than a stone age human. Eventually, they developed time travel, and decided to go back and find out who their creators were. But they went back so far, that they left their DNA in the primordial soup that existed on their planet. And what do you know, a few million years later, their creators evolved, later making a slave race based on what their own ancient ancestors looked like..."

"Ah, bootstrap paradox." Mordin inhaled sharply. "Fascinating. Time travel possible?"

"Possible?" The Doctor repeated. "It's a proven fact! Let's see... It all started when the Time Lord Omega found a star..."

* * *

The Doctor walked into the TARDIS, and slumped down on one of the chairs around the console.

 _'I've run the test again.'_ The TARDIS said. _'What we felt, it_ wasn't _just ghosting.'_

The Time Lord instantly perked up. "Then that means... That means I'm not the last one." Then, something else occurred to him. "How come you didn't figure that out before?"

 _'She's not. At least, not for sure.'_

"But there's only one way to find out." The Doctor said, leaping up from his seat, and setting the controls. He pulled the dematerialization lever, and the TARDIS disappeared, into the time vortex...


	9. The Reveal

_Alternate universes are often tricky business. You'll never know what you'll end up with._

 _You could end up with any number of combinations. A universe where humanity is a race of squid. One where reality is so fundamentally different than yours, that your mind can't physically handle it._

 _Or another, where you were born as a woman._

* * *

Shepard led the team through the loud Afterlife club, to the mercs' recruitment station. The door opened, and she walked inside.

The Batarian recruiter looked up from his terminal. "Well, aren't you sweet?" He sneered. "You're in the wrong place, honey. Strppers' quarters are-"

A bullet hit the wall, only a few inches from his head.

"Show me yours, tough guy." Shepard sneered right back. "I bet mine's bigger."

"So, you're here to fight then?"

"Sure, why not?"

"Standard fee is 500 credits each." The batarian rattled off. "You get paid when the job's done. If you die, your friends don't collect your share. You'll need your own weapons and armor... looks like you've got that covered. And no, this does not make you a member of the Blood Pack, Blue Suns, or Eclipse. You are a freelancer. Period. Any questions?"

"Where do we go?" Shepard cracked her knuckles.

"Just head to the transport station outside the club. One of our boys will take you from there." He said, as he got to looking back down to his terminal. "Send in the next one."

The door opened, and a young man, no more than eighteen, walked in.

"This where I sign up?" He asked.

"Aren't you a little young to be freelancing as a merc? Shepard asked.

"I'm old enough." His voice cracked. "I grew up on Omega. I know how to use a gun."

"Yeah." Zaeed said. "Enough to get yourself killed."

"I can handle myself." The kid continued, getting a pistol out of its holster. "Besides, I just spent fifty credits on this baby, and I wanna use it!"

Shepard's reaction was fast. In a second, she grabbed the kid's arm, and pulled the pistol right out of his hand. "Get a refund." She ordered, throwing the pistol to the ground, and stepping on it, crushing it. "Trust me, kid. You'll thank me later."

Shepard then led the team out of the club, and to the transport.

* * *

The TARDIS engines wheezed and groaned as the ship rematerialized.

The Doctor stepped out of the ship, and onto a beach.

He hadn't been here in many centuries, and he hoped that he would have to again. But nevertheless, here he was.

Dårlig Ulv Stranden, better known as Bad Wolf Bay.

All of a sudden, he felt rippling in the air, and a subtle shift in the timelines.

He ducked back behind the TARDIS, peeking his head around the corner every few moments.

He saw a figure in... Time Lord robes?

The figure was carrying in their arms a small cot, made of very old wood, and probably very ancient.

The Person was concealing their face with what looked to be a bandanna, but he didn't need to see their face to know that what they were doing was breaking their heart. Or hearts.

The Time Lord sat the cot down on the beach, and put something (too small to be a baby) inside. The figure sobbed for a few moments, but gathered themselves, and walked off.

In the distance, a dematerializing TARDIS could be heard.

The Doctor, once sure that the coast was clear, got out from behind his own ship, and approached the cot.

Inside was a baby, no more than a year old. The baby had fairly long curly blonde hair, brown eyes, and a nose of fair size.

The Doctor did a double-take. The hair definitely reminded him of number Six, the eyes of his numerous other selves, and the nose number Four.

The most obvious difference, however, was that the baby was a girl.

The thing that the figure placed inside, was a little gold plaque. On the front of the plaque, was the baby's name in Gallifreyan. On the back, was the baby's name in English.

The Doctor read the plaque, and dropped it back into the cot in shock, running back into the TARDIS.

He came back out, opened the telephone compartment, and called the police.

After telling them about the baby's cries, the Doctor closed the door, and flew off, following the only lead he could think of.

* * *

The skycar that the team was in dipped down, and landed.

The doors opened, and Shepard, Mordin, and Zaeed all stepped out.

"It's about time they send somebody that looks like they can actually fight." A batarian Blue Sun said, approaching them. "They tell you what we're up against?"

"Not a thing." Was Shepard's answer.

"We wouldn't get many volunteers if they knew the truth." The batarian admitted. "Archangel's holed up in a building at the end of the boulevard over there. He's in a superior position, and the only way in is over a very exposed bridge. It's a killing ground. But he's getting tired. Making mistakes. We'll have him soon enough."

"You guys have a plan?"

"A small team is waiting to infiltrate his hideout, but we need to draw Archangel's fire so they can move in."

"And that's where we come in." Shepard guessed.

"Exactly. You'll be on a distraction team. Head straight over the bridge and keep Archangel busy so the distraction team can move in."

"That's goddamn suicide!" Zaeed shouted in response.

"Pretty much." The batarian shrugged. "But you look like you can handle it. Head up to the boulevard and get to the third barricade. Talk to Sergeant Cathka. He'll tell you when to go in."

"Well I'd better go do that." Shepard said, walking away.

"In's gonna be easy." Zaeed told the Commander. "Out's gonna be a bitch."

"We'll figure something out." Shepard told them, as they walked up the boulevard.

* * *

The TARDIS's engines whirred as the ship rematerialized at its destination.

The Doctor peeked his head out of the door, looking around.

Yep, he was in London.

And the airships that this universe was known for flew overhead.

So, that was one point in the 'I'm definitely in Pete's World. Bugger' column.

The Doctor looked around, not having the first clue as to where to start.

He thought about if for a moment, and an idea came to him.

The Doctor closed his eyes, and reached out telepathically.

Instantly, he got a response.

Confusion, uncertainty, and even a little bit of fear was what came back through the link.

Ah, so that meant he was still alive, good. Now all to do was track him down.

The Doctor, spotted an internet cafe in the distance, and decided to start there.

He walked inside, and found a man on a laptop.

The Doctor approached, and presented his psychic paper. "MI6, going to need to... commandeer this computer for a second."

The man sighed, and relinquished his computer.

The Doctor immediately started doing a search for Pete Tyler's whereabouts. He likely knew where Rose was, and Rose likely knew where Ten was.

The Doctor smiled as the search turned up. Turns out, a few years back, the home addresses of every executive of Cybus, and every organization affiliated with it, were leaked.

The address had changed since he was last here, but it was still close.

The Doctor got up, and continued his search.

* * *

"Cathka?" Shepard asked, approaching the batarian.

" _Sergeant_ Cathka..." He stressed. "Ah... You must be the group Salkie mentioned. You're just in time."

"Were you waiting for us?" Shepard asked, a bit on the suspicious side.

"The infiltration team is about to send the signal." Cathka dodged. "Archangel won't know what hit him. Got any questions? This'll be your last chance."

"You coming with?"

"Ha!" Cathka scoffed. "Tarak doesn't pay me to fight. I just plan the attacks and fix this damn gunship. You freelancers get the privilege of-"

Suddenly, the commlink opened, interrupting him. _"Target's in sight. We're a go."_

"Check." Cathka responded. "Bravo team-go, go, go! Archangel's got quite the surprise waiting for him... But that means no more waiting for me. Gotta get her back to a hundred percent before Tarak decides he needs her again." He said, getting back to repairing the gunship.

Shepard spotted a small arc wielder on a crate beside her. She picked it up, and approached Cathka from behind. "You're working too hard." She said, then plunged it into Cathka's back.

"Aagh!" Cathka scream and spluttered as he fell to the floor.

Shepard just walked away, joining the bigger group of freelancers.

The group jumped over the barricade, and began the assault.

* * *

The cab the Doctor was in approached the Tyler mansion, and stopped. The Doctor stepped out, and the cab drove off.

The Doctor looked at the path before him. The Tylers had moved into a place quite far off the grid, presumably so the paparazzi wouldn't bother going out there.

Wouldn't stop him, though.

As he approached the gate, he noticed that it had a quite sophisticated security system, even alien in some places. No doubt installed by his duplicate

Still, it wasn't able to hold back the sonic.

The Doctor stashed the screwdriver in his pocket, and walked right through the front gate.

The Doctor walked up to the front door, and knocked.

"...I swear to God, Pete, if you lock yourself out one more time, I'll-" Jackie Tyler threw open the door, and stopped.

"Jackie!" The Doctor smiled.

*SLAP!*

"Ow!" The Doctor shouted, clutching the right side of his face. "Jackie, it's me!"

"Oh, I knew that!" Jackie shouted right back. Then, she hugged him. "It's good to see you again."

The Doctor pulled himself from her grasp. "Sorry, Doctor not following, Doctor very lost. 'It's good to see you again?'"

"Come inside." Jackie sighed. The Doctor followed her as she led him into the sitting room.

The Doctor stopped once he realized who was present.

His duplicate, Rose, and Jack Harkness(?), were all sitting down, waiting for him.

"Sorry, is this an intervention?" He asked once he found his voice. "I feel like I'm being interventionized."

"Five years." Rose said, a bit angrily. "Five years and you didn't call us back."

"Sorry, _what!?_ "

"The gaps in the universe left behind during the whole reality bomb thing were big enough to allow small things like cell phone signals through. With that in mind we made a prototype interdimensional phone, to keep up with each other, as all families do." Ten said, getting up. "We tried calling you, oh, ten or eleven times?"

"Right, sorry, was having a bit of a companion crisis, myself." The Doctor admitted, a bit sadly. "Nearly ripped the web trying to get them back... It didn't work. The getting them back part, not the web ripping. But never mind that, how's Jack Harkness of all people here?"

"I have my ways, Doc." The former Time Agent smiled.

"He's this universe's Jack." Rose explained. "We met him during the... what was it called?"

"Shakri crisis." Ten finished for her. He then turned the Doctor. "All of these cubes just started appearing overnight. Turns out, they were sent by the-"

"The Shakri." The Doctor finished. "The cubes were sent to prevent humanity from expanding into the stars. Same thing happened over in my universe."

"Right." Ten nodded. "Turns out, the changes to time were having a pretty bad effect on the future, so the Time Agents sent back their best operative to sort it out."

Jack then picked up the conversation. "We got it all sorted out pretty quickly, but my Vortex Manipulator burned out. They probably think I'm dead back home." Rose patted his shoulder lightly. "So, why are _you_ here?"

"I just came from 2158." The Doctor explained. "I saw a Time Lord leave a baby at Bad Wolf Bay."

Ten and Rose sharply inhaled. "And?" Ten asked.

"The baby's name was Theta Sigma."


	10. Archangel

"That... That can't be right." Ten breathed.

"I saw it with my own two eyes." The Doctor told the group. "A Time Lord, a very _skinny_ Time Lord left the cot on the beach. Inside, was a little baby girl, and a plaque with one of our names on it."

"I'm sorry, what's happening?" Rose asked, genuinely confused.

"On Gallifrey, a Time Lord has three names." The Doctor started to explain.

"A private name, a public name, and an Academy name." Ten continued. "The private name is given to you when you're born."

"The public name a few months later."

"The Academy name is the name you pick when you graduate from the Academy." Ten finished. "'The Doctor' is our Academy name."

"'Theta Sigma' was our public name." The Doctor told the other two.

"So that baby girl, was you?" Rose asked, disbelieving.

"Yes. Or at the very least, a baby that had the same name as us." Ten said, then turned to the Doctor. "But why are you telling us this?"

"I came to see if it was yours." The Doctor explained.

Ten looked affronted. "Why would the baby be mine?"

"I don't know, maybe you and Rose got together and did the... thing, after I left."

"Ew, no." Ten shook his head.

"So the baby isn't yours and Rose's?"

"What? No!" Rose raised her voice. She then held up her hand, showing off a shiny golden ring. "I'm married!"

"What!?" The Doctor looked around, confused. "To who?"

Jack raised his hand.

"No, Jack, no questions. I'm trying to figure out who married Rose."

"Uh, Doctor..." Jack said, still holding up his hand.

"It can wait for a few minutes while I figure it out..."

"Doctor!" Rose shouted.

"Eh?"

"It was Jack! _Jack_ married me."

"What? Jack, why didn't you say anything? Never mind that, who'd _you_ marry?" The Doctor directed that last question at Ten.

"What makes you think I'm married?"

"You're wearing a ring. A very nice ring, might I add."

"One of this universe's version of our companions." Ten said vaguely. "That's all you're getting out of me. And we had really better wrap this up, tonight's our anniversary dinner, and she's going to have my head if I don't show."

"Look at you, being domestic." The Doctor smiled. "I tried it myself once, never really got the hang of it."

"Yeah, well I have Donna to thank for that." Ten's face fell. "How's she doing?"

"You mean you know?"

"I'm the Doctor, I always know."

"...She's brilliant." The Doctor said, though Ten couldn't be sure if he was lying or not. "She's married, now. Nice man, nothing like Lance. She's got a kid now, too! ...But I still run into her now and again. Little things. Holding a door open, helping her as a shop assistant, things like that."

Ten just nodded, knowing he'd do the same.

The Doctor stayed silent for a moment, before speaking up. "Well, I didn't get what I came for, but thanks anyway. I've got to get back to the Normandy-"

"No." Rose interrupted. "Stay for dinner, please?"

The Doctor looked over at Ten. "I can invite over S- I mean, my wife."

"Isn't it your anniversary?" The Doctor reminded, trying to weasel his way out.

"We can reschedule." Ten waved off. "Besides, she's been asking me about my 'father' since we met."

The Doctor sighed to himself, and reluctantly said: "Okay, I'll stay."

* * *

Shepard stormed up the stairs of Archangel's apartment, and entered the room that the Turian sniper was in. "Archangel?" She addressed.

The Turian held up his hand in a 'hold on for just a second' gesture. The sniper aimed down the scope of his gun, and pulled the trigger, killing a freelancer that had poked his head out of cover. The turian sat his gun down, and got up. He took off his helmet, revealing-

" _Garrus Vakarian_!?" Shepard asked, using his full name.

"Shepard." Garrus calmly responded. "I thought you were dead."

Shepard pulled Garrus into a hug. "What're you doing here?" She asked, releasing him.

"Just keeping my skills sharp. A little target practice, so to speak." He snarked.

"You okay?" She asked, noticing his not-entirely comfortable demeanor.

"Been better," He admitted, "but it sure is good to see a friendly face. Killing mercs is hard work. Especially on my own."

"How did you end up all the way out here?"

"I got fed up with all the bureaucratic crap on the Citadel." He explained. "Figured I could do more good on my own. Least it's not hard to find criminals here. All I have to do is point my gun and shoot."

"Is that how you pissed off every major merc gang in the Terminus?" Shepard chuckled.

"It wasn't easy." Garrus responded in a sing-song tone. "I _really_ had to work at it. I am amazed that they teamed up to fight me. Guess they really hate me."

"Well, we're here, but getting out isn't going to be as easy."

"No, it won't." Garrus agreed. "That bridge has saved my life countless times... funneling all those witless idiots into scope. But it works both ways. We're going to get slaughtered if we try to go back that way."

"But just waiting isn't a good option either." Shepard continued. "Any ideas?"

"This place has held them off so far. And with the three of you... I suggest we hold this location, wait for a crack in their defenses, and take our chances. It's not a perfect plan, but it's a plan. You think you can handle it?"

"Well, you know the old human saying, right?"

"Which one? There are hundreds."

"I'm ready to kick ass and chew bubblegum. And I'm all out of bubblegum."

* * *

The Doctor awkwardly shifted in his position on the couch.

In the other room, Ten was talking to his wife (whoever that was) over the phone, and Rose and Jack were...

Well, he really didn't want to think about that.

Ten then walked in, throwing his phone on the couch, and flopping down on the piece of furniture. "She's on her way." He said. He then reached under the couch, and pulled out a bottle of wine.

The Doctor raised his eyebrows in a questioning motion.

"I have one of these stashed away at every place I visit on a day-to-day basis." He explained, uncorking the bottle. "It's something I picked up from Donna."

The Doctor smiled.

"So, what've you been up to?"

"Nothing much. Holding back the destruction of the human race. You know, the usual."

"Ah..." Ten nodded slowly. "Who told you about the baby?"

"No one." The Doctor admitted. "I went digging through personnel files, trying to know more about my crewmates."

"Crewmates?" Ten questioned.

"Yeah, I'm sort of helping a woman named Shepard stop a race called the Collectors, back in 2186. They've been abducting humans since 2184, and no one knows why." The Doctor explained. "Anyway, I went digging through every personnel record I could find. In Shepard's, it said that she was left abandoned at Bad Wolf Bay as a baby. I got curious. So I go to Bad Wolf Bay, and see a cot. Guess what was inside?"

"The plaque with our name on it. That means she's..."

The Doctor just nodded. "And yet, she isn't. She has none of our experiences, or knowledge. To her, she's just an ordinary human."

"It sure is going to make things way more complicated when we tell her." Ten said. But the Doctor kept silent, causing Ten to realize something. "You're _not_ going to tell her, are you?"

"Why make things more complicated than they have to be?"

"She _deserves_ to know." Ten said. "How do you think she's going to react when she gets shot one day and then regenerates?"

"She has bigger things to worry about."

"Yes, but that doesn't mean that you can't tell her."

"... I suppose it doesn't." The Doctor admitted.

All of a sudden, knocking on the door interrupted their conversation.

"That's probably my wife." Ten sharply inhaled. "It's unlocked!" He shouted back. He then started fidgeting in his seat.

"Nervous?"

"It's like introducing my girlfriend to my father. Which it is, actually." Ten admitted. "You have met her before... technically."

"Technically?"

"Like I said, our universe's version of her traveled on the TARDIS with us. Just... prepare yourself for a shock."

"Doctor?" A familiar voice called out. "I'm here." In walked Sarah Jane Smith.

The Eleventh Doctor promptly fainted.

* * *

Shepard stormed down the stairs as fast as humanly possible, focused on getting into the basement. Apparently, there were maintenance tunnels that could allow backdoor access into the apartment.

And the mercs had finally decided to use their brains.

So it was a race to the basement, to close all three shutters before the mercs could ambush Garrus.

She closed the first shutter quite easily, but that still left two shutters.

Entering the hall on the left, Shepard was met with a cramped room, storage containers almost blocking the path to the shutter.

Still, it didn't deter her one bit. Vaulting over each set of containers, she fired her assault rifle at those who dared to get in her way.

One of the bullets hit a Blood Pack Pyro's fuel tank, and ignited it, causing an explosion that set everything on fire within its blast radius.

Fortunately, Shepard and Mordin weren't caught in said radius, and Zaeed was still upstairs, helping Garrus hold off the mercs.

Shepard calmly walked over to the shutter, and hit the button.

Ten seconds later, after keeping away the incoming mercs, the shutters closed and locked.

The two headed back the way they came, and entered the other shutter room, but this one was radically different.

Instead of a small hallway, this one was a large loading bay, with multiple vehicles and crates scattered around.

And it was swarming with mercs.

Shepard ducked into cover, and readied her grenade launcher. She took aim, and fired it at small group clustered together.

Switching back to her assault rifle, she took out the ones scrambling into cover with cold precision.

Next, she had Mordin fire an incineration blast at a canister filled with propane or some such gas.

The gas inside the canister ignited as planned, and the container itself exlpoded, releasing all manner of things.

But most importantly, shrapnel. Which, due to its 'slowness' compared to mass effect based weaponry, ignored kinetic barriers, and sliced into the mercs who were standing in front of it.

Shepard broke cover, and sprinted over to the shutter controls. She slammed her hand on the button, and prepared herself for a fight.

More mercs rounded the corner, varren in tow, trying to get through the shutter. Shepard focused her fire on the incoming varren, the fastest and most likely to make it through before the shutter closed.

Then, she focused on the vorcha, using the Pyros' explosiveness to her advantage.

Finally, with the help of a few incineration blasts from Mordin, the remaining Krogan were taken down, before the shutter finally closed.

 _"Get back here, Shepard."_ Garrus suddenly ordered over the comm. _"They're coming in through the doors."_

Shepard acknowledged, and ran back up the stairs.

* * *

The Doctor forced his eyes open, and looked around confusedly. He knew he was in a bed, that was obvious, but he didn't know where. After a few moments, it all came back to him.

The Doctor got up, and ran down the stairs into the sitting room.

The TARDIS was in the corner of the room, the lights in the police box signage pulsing happily as it reflected the ship's mood.

The metacrisis, Sara Jane, Rose, and Jack were all sitting down on the couch, watching the Weakest Link. Rose shuddered as one of the contestants was voted off.

"Oh, sleeping beauty's awake." Jack smiled as he noticed Eleven.

The Doctor instantly tried wiping his mouth with his hand.

"Relax, I didn't try anything _too_ risque." Jack continued to smile.

"Oh, stop it." Rose said.

"Right, well..." Eleven said, looking at the assembled group. "I wasn't expecting this."

"Neither was I." Sarah Jane agreed. "You're technically his father, but you look old enough to be his brother."

"I moisturize." Eleven patted his cheeks, channeling Nine. "How'd the TARDIS get here?"

"I flew it." Ten shrugged. "I noticed that you redecorated." Eleven perked up. "I don't like it."

"Oh..." Eleven's face fell. As the four continued to watch TV, the Doctor decided to explore around the house.

He stopped, as he came to a book in a glass case. The book was very old, most likely dating back two or three thousand years.

" _A Completely Accurate Account of The Shepard Volume Two."_ The Doctor read the book's title. "By... _Professor River Song!?"_ The Doctor produced his sonic screwdriver from his pocket, and aimed it at the glass. He pressed the button, the glass broke, and he pulled the book out. He licked the book's cover, and proclaimed: "This book is from the future." Stating the obvious.

"By how far?" Ten asked.

The Doctor licked the cover again. "Four thousand years. Whoever made this made it to last."

"You're helping Shepard in the future, yeah?" Rose asked, grabbing the book. "So let's see what happens..."

"No!" The Doctor shouted, quickly taking the book away from her. "If you read from a book in the future, detailing events that have already happened from its perspective before they actually happen, then those events become fixed!" He took the book, and somehow stuffed it into his jacket pocket. "The physics of it are very wonky. Heh, 'wonky.' I should say that more often."

"Right, so." Ten clapped his hands together awkwardly. "Dinner."

* * *

"Thanks, Shepard." Garrus addressed the Commander, looking over a dead Krogan. ""They barely got through to me. And we took out Garm and his blood day just gets better and better. He was one tough son of a bitch."

"You knew him?"

"Yeah, we tangled once. Caught him alone. None of his gang to help him. Still couldn't take him out. I've never seen a krogan regen that fast. He was a freak of nature. He just kept at it until his vorcha showed up. It was close, but I had to let him go." Garrus looked down at the body. "Not this time."

Shepard nodded in understanding. "Well, only the Suns are left. I say we take our chances now."

"I think you're right. Tarak's got the toughest group, but nothing we haven't faced before. Besides, he won't be expecting us to meet him head-"

*Crack!* The glass shattered as the gunship Cathka had been fixing earlier hovered up from below.

"Damn it!" Garrus shouted as the group dove to cover. "I thought I took that thing out already!"

"Don't worry about it. A well place shot from a grenade launcher should take care of it pretty easily."

"You didn't... Oh, you did."

Shepard smiled, and readied the grenade launcher. She took aim, and fired.

The shot impacted against one of the engines, and exploded. The gunship shook, but remained steady enough to fire a rocket off.

That hit Garrus in the face.

The Turian dropped to the floor, but the gunship remained.

"No!" Shepard shouted in fury. She took aim again, and fired her shot at the cockpit, this time finishing off the gunship. As the wreckage dropped into the depths pf Omega, Shepard ran over to Garrus.

"Garrus!"

The Turian groaned in pain.

Shepard turned to Mordin. "Radio Joker, make sure they're ready for us!"

"He's not gonna make it..." Zaeed stated sadly.

Shepard seriously hoped that wasn't true.


	11. Christmas With The Doctor

The Doctor awkwardly sat down at the table, thrumming his fingers against the mahogany wood. Sarah Jane and Rose were setting the table, while Jack and Ten were busy helping Jackie finish the food.

But he couldn't help but notice that it was all a little... extravagant. And he voiced his opinion.

"It's Christmas, you plum." Jackie told the Doctor.

"Well where's Pete then?" He asked, looking around.

"Leading Torchwood's busy business." Jack (Harkness) shrugged. "Not that I would know."

All of a sudden, the Doctor stiffened up, as he realized what Jackie had said. "It's _Christmas!?"_ He shot up from his chair, and ran into the TARDIS.

"Oi!" Jackie shouted. "Where are you goin'?"

"Getting presents, I'll be out in a minute!" The Doctor shouted back, closing the door. He walked down the stairs of the console room, and ran into one of the many sprawling corridors. His first stop, was the architectural reconfiguration room.

Approaching the tree-like machine, the Doctor grabbed hold of one of the egg-looking... things, and at the TARDIS's hum of consent, he pulled it off. Then, he moved onto the workshop.

In the corner, was a small cardboard box, labeled: 'K9 Mark V.'

The Doctor sat the egg on top of the box, and picked the box up, heading towards the library.

He walked up to the eighth level, and went over to the corner.

Finding the container marked 'Jack's Stash ;)' he opened it up, and was revolted by what he saw,

Still, the Doctor reached in, and grabbed a few of the 'items' with his hand.

Reminding himself to disinfect that hand later, the Doctor continued to the wardrobe.

The wardrobe was, quite frankly, massive. As big as a mall. Fortunately, that didn't impede his search for another gift.

Stashed away in the back of the wardrobe, was a pair of pink pajamas. He grabbed the PJs, and matching slippers, placed them on the box, and back to his last stop.

If he could remember the way.

'Was it two lefts, a right, half a mile to the elevator, up three floors, through the sun room, past the green slimey wall, and on the right? Or was it three lefts, two rights, through the football stadium, past the swimming pool, down five levels, and across from the sickbay?'

Shaking his head and deciding to let the TARDIS guide him, the Doctor wandered through the corridors, until he came to the large oak doors of the Drawing Room.

He pushed the doors open, and entered. He walked to the desk situated in front of the portrait of his first self, and pulled open one of the drawers.

Inside, was a photo of Rose and his ninth self on Woman Wept.

The Doctor smiled down at the photo, reliving the moment it was taken in his mind. Rose had argued vehemently to get a photo in front of one of the massive ice formations, and nine, after a bit of grumbling, agreed.

The Doctor looked back in the drawer, finding an ornate frame just the right size for the photo. He grabbed it, slid the picture inside, but stopped for a moment. A simple photo wouldn't do, oh no. He had gotten the others all marvelous gifts, and then Rose got a picture.

A lightbulb figuratively popped into existence over his head, and he rushed over to one of the drawers on the wall.

He pulled out a small glass sphere, and a cord that attached to it.

"You think you can get us back home, old girl?"

* * *

"Here we are! Woman Wept." The Ninth Doctor told his two companions, as the TARDIS materialized.

"Woman Wept?" Rose asked, sitting on the seat next to the console.

"Oh, I know this one!" Jack declared, and he then turned to Rose. "It's a planet that all of a sudden broke free from its orbit. In a single" He snapped, "second, everything on the surface froze instantly. The trees as they were being blown on by the wind, the waves, even erupting volcanoes, are all frozen in a single moment in time."

"Figuratively speaking, of course." Nine said. "So, you'd better grab your winter coat. It's going to be just a tad bit nippy."

The Doctor threw the TARDIS doors open, revealing the giant 100-foot tall cliffs of ice, which were former 100-foot tall waves.

"It's beautiful." Rose smiled.

"Ah, yes, hello!" A voice shouted from behind. The voice belonged to a young man, in tweed, who was also wearing a bowtie.

The man was sat on a tablecloth, and was enjoying a pack of Jammie Dodgers. "Come, sit."

The Doctor looked at Jack, who then looked at Rose. The two shrugged, and the three approached.

"Hello, I'm the Doctor." Nine greeted.

"J-" Eleven caught himself, and decided to appropriate someone else's name for the time being. "Jones. Ianto Jones."

"Well, Jones Ianto Jones. What brings a fella like you to a place like this?" Jack smiled.

"Just enjoying a nice picnic by the ice cliffs." Eleven answered. "Jammie Dodger?" He offered.

"More of a banana person, myself." Nine scrunched up his nose.

Eleven held up a finger, and reached his hand into the basket. A moment later, he pulled out a perfectly ripe banana, throwing it to his past self.

He then pulled out a plate of sandwiches, a bowl of mashed potatoes, a turkey, and a cake. "Sorry, this isn't really your normal picnic food, is it? I was kind of in a rush."

"How'd you fit all that in there?" Nine asked, very suspicious.

Eleven winked, and tapped the side of his nose.

Nine's eyes widened.

"What is it, Doctor?" Rose asked. "Who is he?"

"He's... a very old acquaintance of mine." Nine technically lied. Nine reached his hand out, and touched Eleven, getting a nasty shock.

"Doctor, seriously. Who?" Rose asked again.

"Shorted out the differential?" Nine asked. "Timelines out of sync?"

Eleven nodded. "None of you will remember a word of this."

Nine turned to Rose. "He's... me."

"Yeah, very funny."

"No, Rose, I'm serious. Time Lords have this... ability, it's sort of a way of cheating death." Nine explained. "But in the process, I... change. My appearance, personality, even my tastes."

"So he's you." Rose realized. "Does that mean... you're going to die?"

"Everyone's going to die someday."

"But hold on, because if he's you, where are we?" Rose asked for herself and Jack.

"I just came from your house, in the future!" Eleven said, hopping up. "We were about to have dinner, when Jackie said it was Christmas. So I went off to go get everyone a present."

"So, what are you getting me?" Jack asked.

"I thought about a giant cake." Eleven said. "I hid in one of those before, you know. I popped out in the wrong stag party about three times."

"Now _that_ would be one hell of a present."

"I suppose." Eleven shrugged, not really getting Jack's meaning. "But that's not what I'm here for." He reached into his jacket pocket, and pulled out-

"Is that a stasis cube!?" Nine demanded. "Where'd you get that!?"

"I found it in the drawing room." Eleven explained. "It was doing calculations for... something. I don't really know what. Maybe I'll look into it after this is over. But for now..." He reached into the picnic basket, and pulled out a picture frame.

"How'd you fit that in there?" Rose asked.

"It's bigger on the inside, of course." Eleven smiled. He looked around, and spotted a perfect place for the picture to be taken. "The three of you go stand over there."

"Sorry, what's happening?" Rose asked.

"I'm taking a picture, of course!" Eleven said, holding up the stasis cube.

"That doesn't look much like a camera." Jack commented.

"It's not a camera." Nine said. "It's a stasis cube. It takes a single moment in time, and freezes it in a pocket universe. It's what the Time Lords used for art."

"So it's a very powerful camera." Jack said.

"Not quite." Eleven said, directing the three into position. "Just stand there, and I'll do the rest." He ran back over to the stasis cube, and linked it to the frame. He placed his hand over the cube, and said: "Alright, everyone. Say 'Bow ties are cool!'"

 _"Bow ties are cool?_ ' What in God's-" Nine was cut off by Eleven slamming his hand down on the sphere, and a flash of bright white light.

The white blinded the three, and the next thing they knew, they all blacked out.

* * *

The Doctor stepped out of the TARDIS, which had rematerialized in the Tyler household. "I'm back!" He announced, setting the gifts under the tree. All but one.

The other four were assembled at the dinner table, waiting for him.

The Doctor sat down, and then Jack started speaking.

"Good food, good God. Amen."

The five then started digging in.

"You know, it's nice to have a Christmas where aliens aren't invading, and the world's about to end." Jackie reflected.

Eleven looked at Ten questioningly.

"It seems our luck got carried over into this universe, too." Ten answered. "Last year, it was an army of animatronic santas that gained self-awareness. The year before, it was a bunch of mind-controlling game systems. But this year seems to be quite calm, so far."

"So far." Eleven repeated.

The five sat like this for hours, talking for most of it. Jack told of his numerous missions from the Time Agency. Sarah Jane told the story of how she met Ten over in this universe. Ten and Eleven told stories of the mischief they took part in when they were children. Rose had spoke of her involvement at Torchwood. And Jackie had occupied herself with managing Tony, the child she had with Pete.

"Welp, it's getting late." Ten said, getting up. "Me and Sarah should probably head home."

"Home?" Eleven asked.

"You didn't think we lived here, did you?" Sarah Jane asked.

Eleven remained silent.

"You know what? We'll come by tomorrow morning." Ten said. "See you off."

"And me and Rose planned on staying the night anyway, so..." Jack let the sentence hang.

"Oh, it's going to be like a sleepover!" The Doctor said. "What is it you humans normally do at sleepovers? Text? Have pillow fights? Talk about boys?"

"That sort of stuff normally happens over at girls' sleepovers." Sarah Jane told the Doctor gently.

"Unless it's one of my sleepovers." Jack smiled.

Ten groaned, and he and Sarah Jane left. And Eleven, Jack, and Rose stayed up long into the night.

* * *

"...Wake up." The Doctor said, inches away from Rose and Jack's faces.

Rose and Jack screamed, and jumped in surprise, suddenly wide awake.

"Doctor, it's three in the morning. Why are you up?" Rose asked, a bit on the terse side.

"Never mind that, how'd you get in? We triple deadlocked the door." Jack said, pointing to the vortex manipulator strapped to the doorknob.

"Shh!" He gesticulated, placing his hands over Rose and Jack's mouths. "I heard something on the roof."

"You probably heard a bit of snow falling off one of the trees." Rose theorized. "Now go back to sleep."

All of a sudden, a loud clacking came from overhead.

"See? There it is again!" The Doctor whispered.

"...Okay, that was most definitely not snow." Jack threw the covers off of him, and grabbed a pistol taped to the underside of the beside table.

"Is the gun really necessary?" The Doctor asked.

"We're dealing with an intruder." Jack pointed out. "A potentially _hostile_ intruder."

"Argh, fine." The Doctor grunted.

The Doctor and Jack left the bedroom, and tiptoed down the hall. The Doctor and Jack got to the stairs, and peeked over the railing into the living room.

In the chimney, soot fell from above, raining down on the logs.

"He's coming down the chimney." Jack pointed out the obvious, as he pulled the hammer back on his gun.

The logs in the chimney snapped, as the sound of boots hitting the floor was heard.

Then, from the small hole in the mantle, crawled out a large, round man, clad in red and white.

"What the..." Jack looked on amazed, as the man sat a large sack down on the floor.

The man opened his sack, allowing a brilliant golden light to shine out and illuminate the room.

The man reached in, and pulled out a tiny orb of light. The orb glowed brighter, and it transformed into a fully wrapped gift. The man placed the gift under the tree, consumed the milk and cookies, and jumped back up the chimney.

The clacking resumed, as a voice shouted "Merry Christmas!" and faded to silence.

"...What the hell did we just see?" Jack asked.

The Doctor however, was absolutely giddy. "That was _Santa Claus!_ Come on, let's go see what he left!" He sprinted down the stairs, and grabbed a hold of the gift.

The design on the wrapping was very ornate, and read "For The Doctor. Don't Open until Christmas. SC."

The Doctor tried to rip the wrapping paper, but it wouldn't tear in the slightest. He tried again, nearly breaking his fingers as he did so. "Hmm, must be defective..."

"Come on, Doc." Jack rubbed his eyes. "Let's go back to sleep. We can worry about it later."

The Doctor nodded, and they both went back to sleep, and the gift lay unopened under the tree...

* * *

Later, the five had assembled in the living room, and watched as Tony opened his presents. After all the presents were opened, the Doctor stood up, and clapped his hands together.

"Right, there are some other things..." The Doctor began, as he pulled out the presents he got from under the tree. He handed each one to their recipients, and sat back down.

"Oh, Doctor. You really didn't have to..." Sarah Jane began.

"I did." The Doctor responded. "Open it up."

Sarah Jane responded, and peeled the wrapping paper off, revealing the cardboard box underneath. She peeled the tape off the top, causing the sides to fall, revealing-

"Mistress!" K9 greeted happily.

"K9!" Ten smiled.

"Master!" The little robot dog greeted.

"This is brilliant!" Sarah Jane smiled. "Thank you."

The Doctor did a little bow. Next, Jackie opened the one addressed to her.

As she pulled out the pajamas, the Doctor started talking. "Those are made from Betazed silk, softest but strongest silk in the universe."

"Thank you, Doctor." Jackie responded.

Next up, was Jack. He unwrapped it, and smiled. "Thank y _ou,_ Doc."

The Doctor shuddered.

Next, Rose opened hers, and looked down at the picture. Tears started forming in her eyes, as she remembered the day it was taken.

"It's a form of Time Lord art." The Doctor explained. "A single moment in time held frozen in a pocket universe. What you are looking at, is Woman Wept the day we visited it."

Rose, instead of saying thank you, decided to throw her arms around the Doctor.

The Doctor, a bit uncomfortably, returned the hug. Breaking away, he said "Right, the last gift was a bit too big to fit under the tree, so..." The Doctor guided the group outside, to a large box.

Ten approached the box, and pulled the bow, causing all four sides to fall to the ground, revealing a large metal cylinder with a rectangular doorway carved into the side.

"It can't be..." Ten said in awe, stepping forward.

"Why, what is it?" Sarah Jane asked.

Ten ignored her, and pushed the door open, stepping inside.

The Doctor motioned for the others to follow, and they peeked their heads in, prompting a striking realization.

"It's a TARDIS!" Jack vocalized, as he looked around the default white console room.

"How'd you get it to grow so fast?" Ten asked, looking around like he was finally home, which he might as well have been.

"Accelerated time in a localized area." The Doctor explained. "She should be fully grown, but the navigational circuit might be a bit... meh. This one's going to be a chip off the old block for sure." The Doctor patted the console fondly.

"Mind you, I'll have to change the desktop..." Ten commented. "But for now... She's perfect. How about a little maiden voyage? To break her in."

"Ah, but first-" The Doctor ran over to the console scanner, and entered a command. He pressed a button, and the white default console room was replaced with the one that Ten preferred in a flash of light.

"Now we're talking..." Ten nodded in approval.

"Hold on." Jackie said. "You lot can fly this damned thing to Mars or wherever later. There's still one more present under the tree."

The four around the console looked at each other in confusion, before Jack and the Doctor remembered the encounter in the night. The Doctor ran out of the new TARDIS, and dove to the underside of the tree. He pulled out the small rectangular box, and grasped it firmly.

The other four entered just as the Doctor began to peel off the wrapping paper.

As he tore the last bit off, the Doctor looked down at the object in awe.

"What is it?" Rose asked.

"It's..." The Doctor began, looking down the a tablet-looking device. "It's a portable matrix access node."

"Matrix?" Jack asked. "Like those movies from a few years back?"

"No. The Gallifreyan matrix. It was the biggest computer and repository of information in the universe. The whole thing was so large that it existed as an entire pocket universe." The Doctor explained. "But it was destroyed in the Time War, and the resulting connection loss would've fried all devices linked to it, except for a TARDIS. So the question is; How is this working?"

"Hold on, you see that?" Ten asked, pointing to a bit of Gallifreyan writing in the corner. He took his brainy specs out of his pocket, and put them on, squinting at the writing. "Those look like-"

"Co-ordinates." The Doctor agreed. He deactivated the device, and stuffed it in his pockets. "I should probably go look into this." The Doctor hurriedly said, running over to his TARDIS. "But it's been fun."

"Goodbye, Doctor." Ten said.

"Don't be a stranger." Jackie told him.

The Doctor smiled back in response, and entered the TARDIS, setting off into the time vortex.

* * *

 _ **I've been wanting to do a Christmas-themed chapter for some time, but I never got an idea good enough for it. So here you are. Think of it as a late Christmas present.**_


	12. A Rose by Any Other Name

The Doctor shut the door behind him, and moved over to the console. He activated the matrix data node, and fed the co-ordinate data directly into the navcom.

A moment later, the screen displayed the destination created by the co-ordinates, both spatial and temporal.

The Doctor nearly dropped the data node when he realized where it led.

 _Gallifrey, pre-Rassilon Era._

The Time Lords, as their name suggested, had an almost godlike mastery of temporal physics. They could create time locks and loops, they could move an entire star system several thousand light-years all at once, and they could create pocket universes at will. It was the discovery of this technology that ushered in the Rassilon Era, a period of absolute power for the Time Lords.

The Doctor had visited Gallifrey pre-Rassilon Era before, in his first body, before he regenerated for the very first time. It was a period of war and strife among his people, that ended with the invention of the Eye of Harmony. It was a very dangerous period of Gallifreyan history, and would likely be dangerous to go to, even for the Doctor.

The Doctor scoffed at that last thought. _Everywhere_ was dangerous, if he was involved.

He set the controls, and set the TARDIS off into the Time Vortex.

* * *

The TARDIS rematerialized in an alleyway, near the outskirts of a Time Lord city. The Doctor peeked his head out the door, and though he didn't show it, he was nearly moved to tears. Pushing his emotions to the back of his mind, he stepped out of the TARDIS, and looked around.

Judging by the architecture, and relative lack of children, the Doctor guessed that he arrived after Pythia had subjected the Time Lord's to her "Curse." The "Curse" was a sterility plague, similar to the Krogan Genophange, that made birth rates drop. However, instead of reducing the amount of children born, the Curse made it completely impossible for Time Lords to have children biologically. Which led to the invention of the Looms.

Why the co-ordinates led him here, though, he had no idea. He had been here before, at least on his universe's Gallifrey, so why was he led here?

He decided to look around some more. The co-ordinates led him here for a reason, and he was going to find out-

"Grandfather!" A young voice called out. The Doctor turned around, to see a young woman approach him.

The woman threw her arms around the Doctor, and said: "Grandfather, when you threw yourself into the loom, I thought I'd never see you again!"

"Arkyitor, I made you a promise." The words came naturally to the Doctor, as he hugged his/the Other's granddaughter. "And you know me. I _always_ keep my promises."

"But Rassilon-"

"But Rassilon _what_? Rassilon isn't going to do a thing." The Doctor assured. "Like all bullies, he's strong, but so much weaker than he makes himself out to be." He broke the hug, and smiled. "He won't lay a finger on any of you."

"I'm still scared for the others, grandfather." She admitted.

"Well, we all are a little bit, aren't we? Scared for each other." The Doctor said, though this didn't seem to help. "I'll tell you what, I'll leave. Rassilon will think I'm dead, so he'll stop threatening the others, and you'll be the only one to know."

"But where will you go?"

"I don't know. Just away from Gallifrey."

"Then I'm coming with you."

"Arky-"

"It's a big universe out there, and I want to see it."

"Right... If you're coming along, you have to be absolutely sure. After we leave, there's no coming back."

"I'm positive."

"Then let's go." The Doctor led her to the TARDIS, and opened the door.

"It's a TARDIS, how did you get a TARDIS?" She asked, peering inside.

"I borrowed it." The Doctor 'explained.' Out of nowhere, the sound of marching boots were heard closing in. "And that's our cue." He said, shutting the doors. "Help me set the controls."

"I don't know how to fly a TARDIS!"

"Well, there's no better time to learn." The Doctor retorted. He directed her to flick a couple of switches, and as she hit the last one, the TARDIS shook as it entered the vortex. "See? Easy as pi."

"Where are we going?" She asked, with the excitement of a small child.

"Oh, not just where, you see. When." The Doctor said, throwing a lever. "We're going to a starship, called the Normandy, in 2186. They haven't made contact with the Time Lords yet, though, so you'll need to pose as a human."

"I can do that. I might need to change my name though. Arkyitor isn't exactly a normal human name, from what I read... I've always been quite partial to the name Susan..."

The Doctor smiled. "I think it's just perfect."

And then realized why he was led to that particular point in history.

* * *

"Commander, the Doctor's box has reappeared in the cargo bay." EDI reported.

"I'm on my way down." Shepard said, stepping into the elevator. She stepped out, and marched over to the TARDIS. She threw the doors open, and stormed over to the Doctor. "Where the hell have you been?" She demanded of the Doctor.

"I've been on a sort of... personal mission." The Doctor semi-dodged. "Susan, there's someone I want you to meet!" He called into the corridor.

"And you couldn't have told _anyone_ about this little mission of yours?"

"Not really, no. It would've made more questions than answers. Besides, I had expected to return only a few seconds after I had left. But the TARDIS can be a bit fidgety at times."

"Who's this?" Shepard asked, as Susan entered the console room.

"Ah, right. Commander Shepard, meet Susan Foreman. My granddaughter."

"Hello, Commander." Susan greeted.

Shepard raised an eyebrow at the Doctor. "You didn't tell me you were bringing family aboard."

"Well, to be honest, I had a bit of a whim." The Doctor admitted. "Went back to do some investigating, got a bit sidetracked. Ran into Susan, decided to bring her back with me. Thought she could stay on board until the mission's over."

"Uh, she looks a bit young for that." Shepard said, looking Susan over. The Gallifreyan looked to be about fifteen, way too young to serve on a warship.

"What? I'm two-hundred!" Susan argued.

Shepard's eyebrows climbed higher.

"We age differently than humans after a certain point." The Doctor explained.

"Okay..." Shepard said, then she turned to Susan. "We'll get you set up with quarters-"

"I can sleep on the TARDIS."

"-and find you something to do. I'm sure Doctor Chakwas would appreciate help down in the med bay. Now if you'll excuse me, I've got to prep for the next mission." Shepard turned on her heel, and exited the TARDIS.

"She was... nice." Susan commented.

The Doctor clapped his hands together, and changed the subject. "Right, how far were you into your Academy studies?"

"I was just about to make junior Time Lord when we left." Susan said.

Good, now the Doctor had a good idea of where Susan was in her studies. She was only a little bit ahead than his Susan when they stole the TARDIS in their universe. "Okay, the TARDIS doesn't exactly have the standard Academy curriculum on hand, but these should do nicely." He opened a panel under the console, and started pulling books out, which he started handing to Susan, rattling off the names as he grabbed them. "Advanced Quantum Dynamics, Recreational Mathematics, Cosmic Science Volume IIIM, Mechanical Engineering, Flutterwings For Dummies, Type 40 Owner's Manual, and Monty Python's Big Red Book. Hey, I've been looking for that!" The Doctor said, as he pulled out a book named Summer Falls. He placed it at the top of the stack Susan was struggling to keep balanced. "It's a really nice book. I've got a whole collection of stories by the author that did it. I've been meaning to go back and meet her one of these days... Oh, I'm getting sidetracked again." He then pointed to the stack of books. "Go and read up on a few of those. After you're done with all of them, I'll get the TARDIS to give you the graduation test."

Susan nodded, and walked off to the library.

* * *

The Doctor strutted through the Normandy's corridors, and into the tech lab.

"Hello, Doctor." Mordin greeted, looking at the terminal in front of him. "Progress on seeker countermeasure slow, would appreciate possible insight."

"Sure, I've got lots of insight, just call me Mister Insight. Actually no, don't, 'cause that's a rubbish title." The Doctor rambled, moving over to the terminal. He looked down, and noticed something. "What's that?" He asked, pointing to something on the terminal.

"Deep-scan of Seeker biology." Mordin explained. "Seems to be an even blend of technology and biology."

"Well there's your problem. You're looking at purely technological methods that the Seeker would use to stun its victims. Maybe you should be looking at this from a biological perspective."

Mordin nodded, took another sample from the Seeker, and ran it through the computer. A few moments later, Mordin was able to deduce how they worked.

"Seeker paralysis seems to be caused by venom that induces effect similar to biotic stasis field, without need for element zero or dark energy."

"That means it can be counteracted."

"Possibly. Seeker stinger designed to penetrate heavy armor, at the least."

"So increasing the armor density would be pretty much useless."

"Seeker venom also designed to actively fight countermeasures."

"Which means that we would need to counteract the seekers themselves, not their venom."

"Seekers seem to detect targets by seeking out specific vital signs. Could modify armor systems to project non-human life signs. Should make swarms ignore team."

"Unless they start targeting other life-forms." The Doctor reminded the professor.

"Best shot we have at the moment. Will begin preliminary testing. Would appreciate further assistance, Doctor."

The Doctor nodded, and got to work with Mordin.

* * *

"...Okay, everyone, we're here." Shepard announced over the ship's PA. "I know it's not where most of you expected to be, but we've had to take a detour for the moment. While we're here, you should all attempt to get a few hours of shore leave out of it. We'll be heading back out at the end of the day. Dismissed."

"Uh, Shepard," The Doctor flagged down the Commander, "Where is 'here?'"

"The Citadel." Shepard answered. "I got a message from my old CO, Captain Anderson. He wanted to see me, and given that he's the Human Councilor now, I'm not going to dawdle."

"Right." The Doctor nodded. After he got the info he was looking for, he went back down to the cargo bay, and into the TARDIS. "Susan!" He called into the corridors.

"Yes, Grandfather?" Susan responded from right behind him, causing the Time Lord to jump.

"Don't do that!" He shouted, as he snapped his mental barriers into place for some reason.

"Sorry." Susan apologized.

"It's alright. Now, why I came down here in the first place. We're going out." The Doctor said.

"Where?"

"The Citadel! Fine food, art, and-"

* * *

"-and lots of aliens!" The Doctor held his arms open.

"I can't believe it!" Susan bounced on her heels. "I can't believe I'm going to meet actual aliens!"

"You've seen Shepard." The Doctor pointed out.

"Yes, but she's not an alien, is she? These people, though!"

All of a sudden, a shrill scream interrupted their conversation.

"What was that?" Susan asked of her grandfather.

"That, was my cue." The Doctor answered, grabbing Susan's hand, and running to the source of the scream.

By the time the two arrived, C-Sec had already closed the scene down.

"Excuse me, Doctor John Smith, and my assistant, Susan." The Doctor said to the officer, holding up the psychic paper. "We're the..."

"CSIs." Susan picked up the slack.

"Right, the CSIs. We're going to need access to the scene, and for everyone to clear out." The Doctor said, putting the paper away.

Apparently, it was good enough for the officer, as he allowed them in, and ordered the officers away.

The Doctor and Susan approached the scene. "It was a murder..." The Doctor observed sadly, crouching down over the body of a twenty-three year old human woman.

Her eyes were still open, and her face was permanently contorted in an expression of unbearable agony. Her skin was quite literally white as a sheet, and her face was sunken in, almost hollow.

"Whatever did this... it wasn't gentle about it." The Doctor noted. "Right," He began, standing up. "I know what did this."

"What did it?"

"A Plasmavore."


	13. The Bite of the Plasmavore

_**And now, we get to see the Doctor doing Doctor-ish things.**_

* * *

 _"I know what did this."_

 _"What did it?"_

 _"A Plasmavore."_

Susan still looked a bit confused. "What's a Plasmavore?"

"Oh, sorry, forgot you were still new to all this. The universe is absolutely teeming with life, in all sorts of forms. Some feed off plants, others off of meat, some off of energy, and some even eat of pure metal. A Plasmavore feeds off blood."

"Like a Vampire." Susan noted.

"Not quite. See, the Vampires us Gallifreyans fought sucked up blood, and put their own back into the creatures they fed from, thus making more of themselves." The Doctor explained. "Plasmavores, though, they just consume. And they do so in much lower quantities than the Great Vampires. This woman was the Plasmavore's latest catch."

"Then how long until it feeds again?" Susan asked.

"Let's find out." The Doctor said, scanning the body with his screwdriver. "It drained her absolutely dry, there's not a single drop left... How much blood does the human body contain on average?"

"Five-point-one litres." Susan answered instantly."

"Assuming we're dealing with an adult, then taking into account a Plasmavore's average diet, and how human blood tends to sit heavily... Its next feeding should be in about a day."

"A day!?"

"Plasmavores tend to assimilate the blood they consume to blend in with the species around them, but it wears off remarkably fast. If it wanted to effectively blend in, then its next feeding _will_ be in a day. We have to track it down."

"So what should we be looking for?"

"Plasmavores are _internal_ shape-shifters. They can mimic internal physiology, but not external physiology. Meaning who we're looking for looks human, and their next target will be a human. Or a place with sufficient quantities of human blood stored up."

"That narrows it down a little bit, but there has to be lots of humans on this station, and enough blood in case of any incidents. Where do we start?"

The Doctor thought about it for a moment, then snapped his fingers. "The Plasmavore will have to consume blood that doesn't have any sort of diseases present in it. Ebola, Cancer, that sort of thing."

"By that logic, it also shouldn't consume any blood with defects present in the DNA."

"Good work, you're getting the hang of this. But that still doesn't narrow it down enough for us to predict its next target."

"A police force like C-Sec would likely have records of all the crimes on the station, and the evidence associated with them." Susan pointed out. "If we search through their files, we might be able to find a pattern in the victims."

"Excellent idea. I think we passed through a C-Sec checkpoint on our way here. We should be able to access their systems from there." The Doctor guided Susan through the sprawling halls and corridors of the station, back to the Normandy's docking area.

He came to the C-Sec checkpoint, and approached the work area.

"Oh, it's you two again." Captain Bailey greeted. "Is this important, or..."

"Very. I need access to your systems."

"And why would I do that?"

"Because I've-" The Doctor took out the psychic paper, and handed it to Bailey. "-got direct orders from Councilor Anderson."

Bailey's eyebrows raised. "Honorary Spectre Status? I didn't know they still handed those out. But, it checks out. You have your access." He handed the Doctor the paper back, and pointed to a terminal across from him. "That one should be free." He said, getting back to work.

"You keep showing people that like it's your ID." Susan noted once they were out of earshot. "Why?"

"The paper's slightly psychic, so it shows people what I want them to see. I told him that I was acting on orders from the Councilor, so his brain filled in the rest of the blanks for him."

Susan nodded, understanding the principle.

"Here we are!" The Doctor said, as the case files were brought up. He did a search, and found all of the cases that were linked to the Plasmavore (though C-Sec didn't know it) "Let's see, all of the victims are female. They were all in perfect health. All are twenty-one to twenty-five, diplomats and politicians, and they all were found dead on Zakera Ward. But it's still not enough."

"Hold on, look at that."

"What is it?"

"They were all pregnant."

"...You're right. All twenty-three, they were in the last trimester. But why would the Plasmavore only feed off pregnant women?"

"Maybe there's something in the babies' blood that it requires?"

"You know, this might be enough to find he next victim." The Doctor started tapping keys at rapid-fire pacing. "Females twenty-one to twenty-five, in the third trimester, on Zakera Ward, and in perfect health... Got it. There's the most likely one to be the next victim. Angela Morros, age twenty-three, and she's on diplomatic business from Earth, and she's in the third trimester."

"She's the next one?"

"Most likely. Though if the Plasmavore were to take her out, she'd have to start expanding her horizons, and then we'd be back to square one."

"She?"

"Plasmavores can make an approximation of the physiology of the target species from the blood they assimilate, but it's just that: an approximation. A female Plasmavore couldn't pose accurately as a male, and vice-versa. The victims were all exclusively female, so we're looking for a female Plasmavore." The Doctor closed the files on the terminal, and went back over to Bailey. "You need to put a security detail on Angela Morros."

"And why is that?" The Captain responded.

"She's being hunted by a dangerous criminal, and could be attacked at any moment."

"Then consider it done. By the way, I talked with Councilor Anderson, he doesn't seem to remember sending you on this mission." Bailey leaned forward. "Now why is that?"

Okay, he had to come up with something. Fast. "The Councilor's memory has been going...?"

Bailey was not amused.

"Fine, you caught me." The Doctor held up his hands, then producing the paper again. "I'm with a secret branch of Alliance Intelligence, named..."

"Monty Python." Susan cut in.

"Yes, right, that. I'm their top operative, codenamed the Doctor. This is my assistant, the Foreman."

"Given that you lied to me the first time, what makes you think I'll believe you this time?" Bailey asked.

"Because you want these murders stopped as much as I do. And I'm the only lead you have." The Doctor responded.

"I could get Shepard down here to sort this out."

"Let's be honest, you really don't want that kind of attention, do you?"

"..." Bailey stayed silent for a moment. He typed a few commands into the terminal, he then looked up. "I've given the go-ahead to the security detail. Go. Stop the bastard responsible for this."

"Then consider it done." The Doctor responded, leading Susan out.

"'Monty Python?'" The Doctor asked, incredulous.

"'The Foreman?'" She questioned right back.

"Oh, shut up."

"Grandfather, how are we going to find the Plasmavore?" Susan asked after a moment.

"The Sonic should be able to detect the life-signs of a Plasmavore quite easily. Even if it's posing as a human, there's still a little bit of residual DNA. The problem is the signal range." The Time Lord elaborated. "We'd need a transmitter as big as a skyscraper to scan the entire station at once."

"What about that?" Susan suggested, pointing to the large structure at the center of the Presidium ring.

"That might do... If my history of this universe is correct -and I've been doing some reading in my spare time, believe me- that tower acts like a big transmitter, coordinating the Keepers and the station's critical systems. If we can get up to it..."

"Then we can find the Plasmavore!"

"Then there's no time to waste! Come along, P-... Susan!" The Doctor grabbed Susan's arm, and proceeded to the Presidium.

* * *

"This meeting would be much more productive if Udina were here." The asari councilor said.

"My _advisor_ is unavailable. As Councilor, I represent the voice of humanity and the Alliance." Councilor Anderson stressed. "Shepard will be here at any-" The door to Anderson's office, and the person in question walked in. "Oh, Commander!" Anderson greeted. "We were just talking about you."

"Nothing bad, I hope." She smiled. "It's been a long time. The last couple of years been treating you well?"

"There's been some rough spots." He admitted. "But it's good to have you back."

"We've heard many rumors surrounding your unexpected return." The salarian councilor interjected. "Some of them are... unsettling."

"We called this meeting so you could explain your actions, Shepard." The asari councilor explained. "We owe you that much. After all, you did save our lives."

' _Damn right I did.'_ Shepard reflected to herself. Then, she started speaking aloud. "The Collectors are the ones abducting human colonies out in the Terminus. Worse, they may be working for the Reapers."

"The Terminus systems are outside our jurisdiction." The turian councilor tersely responded. "The colonists knew this when they left Council Space."

"You're missing the important part." Anderson rushed to Shepard's aid. "The Reapers _are_ involved."

"Ah yes, 'Reapers.'" The turian councilor air quoted. "The immortal race of sentient starships allegedly waiting in dark space." He scoffed. "We have dismissed that claim."

"Shepard, no one else encountered the VI on Illos that told you the truth about the Reapers." Anderson elaborated. "Only you and your crew ever spoke with Sovereign. I believe you, but without evidence from another source, the others think Saren was behind the attack."

"But it's obvious the technology from Sovereign is too advanced to be geth!"

"We have not found any evidence to suggest that it _wasn't_ a geth creation." The salarian councilor illuminated.

"The geth are capable of remarkable technological achievements." The asari councilor interjected. "Which is most likely why Saren recruited them."

"This 'Reaper' theory proves just how fragile your mental state is." The turian councilor directed at Shepard. "By Cerberus, and before them, by Saren."

"Okay, but Saren was an organic. There's no way the geth would willingly follow him!"

"Saren was a compelling an charismatic individual." The asari councilor argued. "He was capable of convincing the geth the Reapers were real. Just as he convinced _you."_

"It was part of his plan to attack the Citadel. The Reapers are just a myth." The turian councilor waved off. "One you _insist_ on perpetuating."

The asari councilor was at least a bit more diplomatic. "We believe that you believe it, but that does not make it true."

"I kept Saren from conquering the Citadel." Shepard clenched her fists. "I sacrificed human lives to save this council. And this is what I get?"

"We are in a difficult position, Shepard." The asari councilor said. "You are working for Cerberus, an avowed enemy of the council. Not to mention a Time Lord."

Shepard's blood froze, though she didn't show it. "What does he have to do with this?"

"The Time Lords nearly wiped out galactic civilization as we know it almost eight-hundred years ago." The salarian councilor explained. "We managed to cover it up as part of the Rachni Wars, as they were happening at the same time, but the Time Lords destroyed nearly three-hundred worlds, and killed countless innocents. The only reason we are still alive today, is that they suddenly retreated for no visible reason."

"And _why_ do you assume _I'm_ working for _him_?"

"A Time Lord would not stoop so low as to work for what they perceived as 'lesser species.'"

"Okay, first of all, that man is a part of my team." Shepard pointer her finger, getting angry all of a sudden. "Second, and even if I wasn't, I'm a nice person, and so's my granddaughter. Finally, without me, there would not have been a Citadel Council in the first place!"

The councilors looked confused. "And what, pray tell, is that supposed to mean?" The asari councilor inquired.

"You know what I mean, without me, the Asari wouldn't have been able to crawl out of the primordial muck, let alone find and colonize an ancient space station!" Shepard, after she had stopped talking, realized what she had said. But she didn't say it."I'm sorry, I-"

"Well, it seems that your mental state is much more fragile than we realized." The asari councilor huffed. "We cannot afford to occupy our time with this any longer. This meeting is adjourned." All three holograms flickered, and died.

"What the hell was that!?" Anderson demanded.

"I don't know, sir." Shepard truthfully stated. To her, it felt like she had been kicked out of the driver's seat, and a far more experienced driver took over for a moment. She knew what she said, but she didn't know what motivated her to, and why. "I feel like I'm going insane. Ever since the Doctor appeared on board the Normandy, I've been having these... dreams. And that part right there felt like I was talking _as_ him."

"Wait a moment, did you call him the Doctor?" Anderson questioned. "Are you sure?"

"Yeah. Is that important?"

"The Doctor is... it's hard to put what he is into words. And I'm not just talking about his species."

"You know something about him?"

"It's not much." Anderson admitted. "But then again, so is the intel we have on him as a whole. He's saved the Earth dozens, possibly even hundreds, of times, and that's about all we know. You know the Cyberman incident?"

"What little I could get with my spectre clearance." Shepard answered. "Why?"

"He was the one that put a stop to it. It's like that all throughout history. He appears at a random place and time, and keeps things going well for the human race. The Titanic disaster? Eyewitness accounts pegged him as carrying children into lifeboats, and helping people still trapped on the lower decks. The 2012 Olympics torch bearer? The one that made everyone in the stadium reappear after they vanished? That was him. There's even stone carvings of him recovered not too far from Pompeii. The Doctor is humanity's own guardian angel, and if he's shown up again, then massive amounts of death and destruction are about to follow. As long as that man is here, the galaxy's in danger."

"I fail to see how that's any different than normal."

"You may be right. For all we know, he could be here in response to the incoming Reaper invasion. But for all we know, his mere presence could also be causing it. Time Lords are tricky like that. Just promise me you'll be careful around him."

Just then, wailing sirens from multiple C-Sec skycars brought them out of their conversation. Shepard looked at the lead skycar, a yellow monstrosity, to see her HUD tag it. 'THE DOCTOR' the tag read.

"And that's him, now." Shepard groaned, looking up. "I tell him to do one thing, just one: Don't get into trouble. Is that too much to ask?"

"What in heaven's name is he doing?" Anderson asked, as the skycar dove and did a U-turn, causing the pursuers to be disoriented for a moment.

Shepard closely studied the Doctor's pattern, and then realized something. "He's not trying to shake them, he's trying to distract them. But from what?"

* * *

Susan stalked through the corridors of the Presidum Tower, careful to evade any guards and the like. The Doctor hadn't been too receptive to her volunteering to use the transmitter, but once she reminded him that it was either this or piloting a skycar in a dangerous attempt at a distraction so one of them could get into the tower, he had caved.

Fortunately enough for her, the tower seemed to be empty. So far.

Now, all she needed to do was find a master control terminal of some sort. Calling upon the standard training for sonic devices, Susan scanned around for a computer that linked to all of the tower's systems.

After a few seconds, the screwdriver beeped back, and increased the pitch of its frequency, homing in on the terminal's location. As Susan turned, the screwdriver increased the frequency itself, until it became nothing more than a steady whine.

With the location of the terminal figured out, Susan approached, changing the setting on the device, and pressing the activator.

A large holographic screen appeared at the end of a walkway suspended over a small pit. Susan approached it, and studied it for a moment.

It seemed that the terminal could be used to access a great deal of the Citadel's systems, those most of those functions were locked out. Fortunately, the function controlling the Presidium Tower's transmission capabilities were unlocked.

Susan pointed the screwdriver at the terminal, and pressed the activator again. This time, the frequency being transmitted by the sonic was far too high to be heard by any organic, though it still reverberated throughout the station. A moment later, the search results were in.

And apparently so was security, as Susan heard the sound of opening doors. Susan deactivated the terminal, and hightailed it out of there.

* * *

"Oi, that last one could've hurt someone!" The Doctor shouted out the window, as the shot from a C-Sec shuttle missed the car, and hit the Presidium grounds below. As he looked down at the car's control panel, he noticed an incoming call, and pressed the button to accept it.

 _"What the hell are you doing!?"_ Demanded the furious voice of Shepard.

"I'm trying to make a distraction, what else does it look like?"

 _"I guessed that, but why!?"_

"Susan and I are looking for a dangerous criminal, long story. She needed to get into the Presidium tower to scan for it, so I needed to make the distraction." *Boom!* "Oh, and not to worry you or anything, but I think I've just been shot down." The car started smoking and veering wildly out of control.

 _"Dammit."_ Shepard cursed. Then, she seemed to focus her attention to someone else. _"Anderson, tell C-Sec that he's good."_

 _"I can."_ Anderson responded. _"But it's entirely up to them whether they want to listen or not."_

"You two better hurry up. Because I think I've just crashed." He said, as the car finally hit the ground, and slid for another few meters before it came to a stop in front of the Relay Monument. "Another happy landing." He said to himself, as he opened the doors, and stepped out.

Into a waiting squad of C-Sec, apparently.

"Hands in the air!" A turian officer barked at the Doctor, as he and the other officers leveled their guns at the Time Lord. "Now!"

"Come on," The Doctor said, putting his hands up. "Is there any real need for the shouting? And the guns?"

"All of you, stand down!" Anderson shouted to the officers, as he and Shepard ran up to them. "Doctor Smith's with us."

"That may be, Councilor, but he broke at least thirty laws pulling that stunt!" The turian responded.

"I said, stand down!" Anderson ordered.

The turian officer sighed, and gave the order to stand down.

"Now, here's what's going to happen next:" Anderson started. "You and your men are going to turn around, leave, and never mention this to _anyone_. Not even in a report. Doing so is tantamount to treason."

"Yes, _sir."_ The turian officer gritted his teeth, and he and his men retreated.

"Come on, let's go back to my office." Anderson said, as he led the other two back.

One they were in, and the door was shut, Shepard turned to the Doctor, and blew up. "What the hell was that!?"

"I told you, me and Susan were looking for a dangerous criminal." The Doctor responded, a bit put off.

"And you couldn't have told me this at all!?"

"Well, considering the criminal we're looking for is in essence a vampire, no." Then, the door opened, and someone walked in. "Ah, Susan! You've got the scans?"

"Every last centimeter of the station was scanned, Grandfather." Susan answered, handing the screwdriver back.

"Hold on, how'd she get in?" Anderson asked.

"It's a Time Lord trick."

"Oh, really?" Shepard rhetorically asked. "What kind of-"

"Shh..." The Doctor quietly said, making the 'shh' gesture.

Shepard abruptly stopped talking in her tracks, suddenly finding that she forgot how to talk. A moment later, she returned to normal. "What the... Can you teach me how to do that?"

"Probably not." The Doctor said, intensely looking at the sonic screwdriver. "That's not good... The security detail!"

"Wait, what about them?" Susan questioned.

"They're in danger!"

"Well, given that they're a security detail-"

"No, not that kind of danger, Susan. Angela's the Plasmavore!"

* * *

"Hold on, there's a vampire disguised as a human diplomat loose on the station?" Shepard asked, not believing. She, The Doctor, and Susan were running through the station to try and find the person they were looking for.

"Not just a Plasmavore." The Doctor reminded. "A _pregnant_ Plasmavore. That's why it was only drinking the blood from pregnant people, Susan. Plasmavore children can't form naturally without some kind of assistance, consequences of consuming blood you see. The Plasmavore needed the developmental hormones carried in the babies' blood."

"But why only target the politicians and diplomats?" Susan wondered.

"She was probably taking out the competition while she had a chance. Two birds with one stone." Shepard said. "Here's her office." She said as they approached. The door opened, and the three walked into a small room, with the various things you'd expect a politician to have, and then four dead C-Sec officers, lying on the floor in a heap.

"We're too late..." The Doctor observed. "It's all my fault. I told them to guard her, and they got killed because of it..."

"How long have they been dead?" Shepard questioned.

"The last one to have had this done to him has been dead for no more than... three minutes. We can still catch her!" The Doctor shouted, getting the screwdriver. He acivated it, and held it close to his eyes. "She's heading towards C-Sec! Come on!"

The three left the office, and ran back through Zakera Ward to the C-Sec station.

"Where is she?" The Doctor asked Bailey.

"She turned herself in." The Captain responded. "She's over in interrogation room two, if you want to talk to her."

The Doctor, Susan, and Shepard were all confused. Wasn't she trying to kill them? Deciding they could get answers from the source, Shepard led the team into the room.

Inside, was a small woman. About twenty-three, curled up into the fetal position on the floor, and rocking back and forth, murmuring: "I didn't want to... I didn't want to..."

"Hey." Shepard said, leaning down. "Are you alright?"

"Please, I didn't want to..." The Plasmavore sobbed.

"Oh, of course." The Doctor seemed to realize something. "It all makes sense. That baby, I'm guessing you don't know the father?"

"Doctor, you can't just ask something like that!" Shepard responded.

But the Plasmavore just silently nodded.

"And your family disowned you because of it?"

The Plasmavore nodded again.

"So she's twenty-three and got into a one-night stand, and got the short end of the stick for it." Sheprd realized.

"No." The Doctor shot that idea down. "Plasmavore society is a bit different than humanity's. The closest analogue to what happened to her in human culture would be a sixteen year-old, still in school and doing teen things, getting pregnant with no idea who the father was, getting disowned because of it, and then running away to save her the embarrassment of having to look at the people she knew. In fact, that's exactly what happened. That's why she needed the others. The closest star system that can offer a Plasmavore proper prenatal care is in the Andromeda galaxy. This isn't a ruthless criminal causing misery for the hell of it, this is a mother doing whatever it takes to keep her baby alive." The Doctor approached the Plasmavore. "Hey, listen. It's going to be alright. I know you didn't want to do what you did, and I'm going to help."

"But, why?" The Plasmavore asked.

"...Because I know why you did it. And I can sympathize. I'm going to help you get what you need, I promise." The Doctor said, standing back up straight. "Come on." He said to Susan and Shepard. The three left, and once the door closed behind them, the Doctor pulled a cellphone out of his pocket.

"Who are you calling?" Shepard asked, recalling the function of the device.

"The proper authorities." The Doctor answered, then started speaking to the person on the other end. "Yes, hello, this is the Doctor. I have a Code 76-23D, Giving you my coordinates now." He said, tapping something into the phone's touchscreen. "Yes, a Plasmavore. Twenty-three. In the third trimester. These people don't have teleport shielding. Okay. Alright, goodbye." The Doctor stashed the phone in his pocket, and the three walked out of C-Sec.

"Who was that you called?" Shepard inquired.

"The Shadow Proclamation." He answered. "Sort of a posh way to say 'outer space police.' They hold jurisdiction over a hundred galaxies, including this one. And they've dealt with this sort of thing before."

"What about the Plasmavore?" Susan wondered.

"They're coming to take her back to her homeworld, located in the Isop Galaxy. She'll be confined to it for the rest of her life, but it could be worse."

"Hold on, you're letting a proven murderer get away scot-free?" Shepard asked incredulously.

"She was a mother, doing what it took to keep her baby alive." The Doctor said. "Wouldn't you do the same?"

"Let her go, or do what it took to save my child?"

"Yes." The Doctor clapped his hands together. "Right, I don't know about you lot, but after doing all that, I feel kind of hungry. Care to join me?"

"I'm in." Shepard shrugged. "As long as it's not blood."


	14. The Convict

"Freedom is the right of all sentient beings." The Doctor watched Optimus Prime say on the giant wall-sized TV in the lounge.

The TARDIS lounge was a large theater sized room, filled the the brim with various entertainment... things, from all corners of the universe. The Doctor and Susan were lounging around, as the Normandy flew through space to its next destination.

"Grandfather, could you turn that down?" Susan requested, reading a book at a desk.

"It's Transformers!" The Doctor made the sound with his mouth. "My Eighth self used to love this show!"

"Still, I'm trying to concentrate on this." Susan responded. But something kept bugging her. "Eighth? Did you really regenerate that many times?"

"More, actually. I'm the Eleventh."

"Oh... Does it hurt?"

"Does what?"

"Regeneration."

"Not really. It kind of feels like a bad LSD trip. Don't ask how I know that." The Doctor said. Just then, Shepard walked in.

"Hello, Doctor." Shepard greeted. "Nice chair."

"It is, isn't it?" The Doctor rubbed the velvet. "But that's not why you came here."

"Very observant of you. We're going to recruit the next teammember. I want you to come with, give you another chance to prove yourself."

"Ah, yes, good idea!" The Doctor hopped up. He then turned to his granddaughter. "Stay here and keep studying. Don't answer the door for anyone, even if they knock. I'll be back before you can say 'Where's he gone now?'" The Doctor said, following Shepard out of the room. "Not that fast!" He shouted, peeking his head in. "But pre-tty fast." He said, finally leaving.

Susan sighed, and got back to her studies.

* * *

 _A few minutes earlier..._

"Shepard, you can't be serious!" Miranda said, following the Commander, who was heading down to the cargo bay. "He contributed nothing to the mission last time!"

"I want to keep him where I can see him."

"But he's useless!"

Shepard stopped, and fixed Miranda with an icy glare. "I take offense to that."

Miranda was understandably confused. "Why do you? You said it in the mission reports yourself."

Shepard stopped glaring once she heard Miranda's point. "I did, didn't I...?" Shepard sighed. "Ever since I stepped into that box of his back on Omega, I've felt like I'm going insane. There are these dreams I keep having of... it was me, but it was also not me, founding an entire civilization! And then, back on the Citadel, I had an outburst at the Council, and told them that I was responsible for the Asari's evolution!"

"And you think that he's connected somehow?"

"It's the only thing that makes sense." Shepard said as she and Miranda entered the elevator. "That box of his has some pretty... unique properties."

"What kind of properties?"

"Oh, you'd just love to learn the details of eleven-dimensional vortex science, wouldn't you?" Shepard snorted, then froze. "Now you see why I want to keep him in my sight!?"

"You think he's doing this to you on purpose?" Miranda asked. "Perhaps you should go to Doctor Chakwas, and have her run some tests."

"I will." Shepard said, stepping out of the elevator. "After the mission." She amended, approaching the TARDIS. Shepard opened the TARDIS door just enough for her to slip inside without Miranda seeing the interior. Shepard locked the door, and proceeded over to the console. "Doctor!" She shouted. "Where is he?"

As if responding to Shepard's question, one of the monitors above the console switched on, and showed an interior layout of the TARDIS. Two rooms were higlighted, one in blue, the other in white. The white one seemed to be the console room, and the other looked to be where the Doctor was.

"Uhh, thanks?" Shepard awkwardly looked at the time rotor. She shook her head, and proceeded into the sprawling corridors, intent on finding the Time Lord.

* * *

 _In the present..._

The Doctor shuddered as he and the others left the Normandy and boarded the prison ship, Purgatory, where their next recruit was located. Though their similarities may have been distant, at best, the Doctor couldn't help think of Shada, the legendary Time Lord prison where only the worst of the worst were sent.

Still, he followed the the others deeper into the prison.

"Welcome to the Purgatory, Shepard." The guard greeted as they approached. "Your package is being prepped, and you can claim it shortly. As this is a high-security vessel, you will need to relinquish your weapons before we proceed."

Shepard narrowed her eyes in suspicion. "I'll relinquish one bullet." She threatened, drawing her pistol. "Where do you want it?"

"Everyone stand down!" A turian shouted, entering the room."Shepard, I'm warden Kuril, and this is my ship." He introduced himself as he approached the waiting group. "You must realize that this is a standard procedure. Your weapons will be returned to you on your way out."

"Yeah?" Shepard sarcastically asked. "It's my standard procedure to keep my gun."

The warden's stare was piercing, but Shepard didn't waver. The others readied their weapons, and the Doctor's grip on the sonic screwdriver tightened. He put it on setting #38557879b, ready to make the guns short out in their wielders' hands.

Fortunately, it didn't come to that, as the warden backed down. "Let them proceed." The warden ordered his subordinates. "Our facility is more than prepared to handle three armed guests."

Shepard, Miranda, and Zaeed holstered their weapons, and the four followed the warden through the large blast door, deeper into the ship.

"Cellblock two." The warden identified. "As you can see, we keep a tight hold on the population."

Through one of the windows the corridor was lined with, the Doctor could see a pylon powered by element zero activate, creating energy bubbles around fighting prisoners, separating them.

Then, a massive crane arm swung down from the ceiling, and attached to a small cubic container, pulling it out of a wall made out of similar containers. The arm then swung around to attach it to a door, further down the hallway.

"Each cell is a self-contained modular unit." The warden elaborated. "I've blown a few out of the airlock as an example before. This ship is made up of thirty cellblocks identical to this one. And each cellblock holds thousands of criminals." He boasted. "We can put the whole place on lockdown at a moment's notice."

"I've seen better." The Doctor shrugged. It was true, some of the prisons (especially the ones designed to hold Time Lords) back in his universe would make this place look like an open door.

"I'm sure." The warden condescended.

"It's got to be expensive as hell to run a place like this." Shepard observed.

"We can cut corners that governments can't." The warden elaborated. "And each prisoner brings in a fee from their homeworld. These people are violent, and their homeworld pays well to keep them here."

"And what happens if their homeworld doesn't pay the fee?" Shepard crossed her arms.

"Then we inform them that we can no longer afford to keep the prisoner, and have to release them." The warden answered. "At an unspecified place and time."

"So it's an extortion racket." The Doctor spat, disgusted. "Despicable."

"You don't have to agree with my methods, but _don't_ mistake my intentions. These are despicable people, and I'm keeping them locked up."

"How'd you end up running a place like this?" Shepard questioned.

"I was in law-enforcement back on Palaven. I got sick of seeing criminals escape into the larger galaxy, and bounty hunters aren't dependable. Eventually, I got an idea: Keep the criminals in space, and the galaxy is a safer place."

"So you do all this because you think it's necessary?" Shepard asked.

The warden nodded. "Every day I see the _worst sapient life_ the galaxy has to offer. Governments are soft, unwilling to make the hard choices. Someone had to stand up and make the galaxy safe."

"And because Jack's here, I assume he's on that list." Shepard shook her head in frustration. "What can you tell me about him?"

"Cerberus hasn't told you?" The warden asked, twiddling his thumbs. "Jack is the meanest handful of violence and hate I've ever encountered. Dangerous, crazy, and very powerful." The Warder, said in fear. "You'll see soon enough."

"Alright, let's get on with this." Shepard said, uncrossing her arms.

"Bet it'd be hell trying to escape from this place." Zaeed remarked.

"We're in space." The warden said, leading the four forward. "They have nowhere to go, and they know it. But still, we exercise extreme caution. These are... dangerous individuals." A door slid open, and the warden led the group into an almost identical hallway. "I'm going to confirm the funds from Cerberus cleared. Outprocessing is straight down this hallway." He guided. "Just keep going past the interrogation rooms and the supermax wing." He lingered for a moment, then left. "I'll catch up with you later, Shepard."

"I don't like the way this place is making me feel." Shepard said after the warden left. "Everyone be on your guard." Then, she started leading the team down the hallway.

As they were walking, the Doctor noticed something. A cell was attacked to the hallway, and inside, a guard was beating the prisoner. "Is this really necessary?" The Time Lord demanded.

"Compared to what he did to his victims, this is a light massage." The guard outside the cell responded.

"If you keep doing this, it makes you no better than him." The Doctor told the guard. "Besides, don't you get tired of it?"

"...I admit, I kind of do." The guard reluctantly admitted. "I wonder, is this really getting us anywhere?"

"Then stop this." The Doctor pointedly told. "For your own sake." Then, he caught up with the others, who had just crossed the threshold into outprocessing.

The four approached the door on the far side of the room, and opened it.

Instead of what the four expected, they were met with one of the cells used to store prisoners. _"My apologies, Shepard."_ The warden's voice rang from overhead. _"You're more valuable as a prisoner than a customer."_

"Kuril," Shepard cracked her knuckles, "you've just kicked the hornet's nest. And now, you're about to get stung."

 _"Activate systems!"_ The warden ordered. At that instant, numerous Blue Suns entered the room, firing their guns at the four, who scrambled into cover.

A FENRIS mech charged into the room, and the Doctor, seeing his opportunity, took it. He pointed the screwdriver at the tiny robot, and pressed the activator, causing the mech to spark, and then go running back to its owners. The mech then triggered an EMP, and knocked out the shields of the assembled Blue Suns.

"Excellent work, Doctor!" Shepard shouted as she fired upon the Blue Suns. After the last one was dispatched, the four ran out into the hall, taking care of the other two Blue Suns that tried to stop them. Shepard opened the door into the cryo chamber, and entered.

"Shepard is on the loose!" A techie shouted frantically. "I repeat, Shepard is- aagh!" Shepard shot the man right through the hart, and watched coldly as his body toppled to the floor.

The Doctor didn't comment on any of it, just settling to watch as the Commander approached the controls.

"If we hack that control, every cell on board opens." Miranda warned.

"It's the only way to get Jack out of cryo." Zaeed said.

"Oh, that's a rubbish word, 'only.'" The Doctor rambled, approaching the controls. "There are always alternatives to situations." The Doctor looked over the controls. "Should be a cakewalk for the sonic." He ran the device over the terminal, and grinned. "There, you can press it without popping open every other cell on board."

Shepard nodded, and slammed her hand down on the button.

In response, three YMIR mechs below activated, and a big metal arm with two prongs extended down from the roof. The arm inserted its two prongs into two similarly sized holes in the floor, and rotated. The arm then pulled up a cylinder, with something resembling an examination table inside.

" _That's_ Jack?" Miranda asked, looking at the frail, heavily tattooed female form cuffed to the table.

Jack's eyes snapped open, and the woman looked around the room. Her expression changed to fury, and she started pulling herself out of the cuffs, breaking them in the process.

Jack fell to the floor, and saw the three mechs approach. She gritter her teeth, and dark energy started gathering up around her fist in a blue aura. Jack, howling a primal roar, charged towards the mechs, decimating them in an explosion, which consequently shook the floor beneath them.

"That was impressive." The Doctor looked down at the room in awe.

"We have to get down there, let's move!" Shepard led the group through the door, and down the ramp into the cryo storage area.

On the other end of the room, the wall was ripped open, creating a passageway into the other areas of the ship. How could someone so small create so much damage?

 _"All guards, restore order!"_ Kuril shouted. _"Lethal force authorized, but don't kill Jack! Techs, lockdown, lockdown!"_

 _"Sections seven, nine, and eleven have lost life support."_ The Purgatory's computer reported, without a hint of emotion. _"No survivors."_

The four walked through another hole in the wall, into the cellblock, where the prisoners that hadn't been in their cells when Jack was released, along with the guards, were fighting. The red emergency lighting was on, fires were everywhere, and the ship was crumbling as the four made their way through.

 _"All prisoners, return to your cells immediately, or I'll open every airlock on this ship!"_ The warden threatened.

On the other side of the cellblock, a YMIR mech activated to supress the fighting.

"Doctor." Shepard pointed out.

The Doctor nodded, aimed the screwdriver at the mech, and pressed the button, causing the two-ton behemoth to explode, after it had already taken down the unarmed prisoners.

The four got out of cover, and proceeded forth.

 _"Warning: All reactor core safeguards are now non-functional. Prepare for reactor meltdown."_

The four walked into another cellblock, where the guards were waiting for them. Shepard fired at the canister on the walkway above them, causing it to explode, and set fire to the two guards next to it.

The four proceeded through the ship, taking out more guards as they came across them.

Eventually, the four entered the final cellblock, where the warden was waiting for them.

"You're valuable, Shepard." The warden said, firing at them, but missing. "I could have sold you and lived like a king! But you're too much trouble. At least I can recapture Jack."

"Not happening!" Shepard shouted back. "You're a two-bit slave trader, and I don't have time for it."

"I do the hard things civil governments are unwilling to. This is for the good of the galaxy!" He argued. Then, three energy pylons activated, powering a shield that protected the warden, while more guards came in.

"Doctor, you take out one of the pylons, while me and the others take out the rest!" Shepard ordered over the gunfire.

The Doctor nodded, and sprinted out of cover, ducking and dodging the bullets that came his way.

Across the room, a grenade detonated, taking out a pylon. Then, another one of the pylons was subject to an Overload.

Finally, the Doctor pointed his screwdriver at the pylon, and pushed the activator, causing the pylon to short out.

Shepard and the others then focused their fire on the remaining guards, before directing it to the warden.

His shields couldn't handle the fire, and his armor was torn through by an inferno grenade, before he finally dropped dead from his wounds.

"Come on." Shepard said. "We can still catch up to Jack."

She led the others through the halls, following the path of destruction, finally coming to a stop once they found Jack screaming in rage at the Normandy.

Shepard saw a guard trying to run towards Jack. Shepard fired her pistol, which took out the guard, and also had the effect of getting Jack's attention.

"What the hell do you want?" Jack spat.

"You're in a bad situation, and I'm here to get you out of it." Shepard answered nonchalantly.

"Shit, you sound like a pussy." Jack chuckled. "I'm not going anywhere with you. You're Cerberus."

"The dog?" The Doctor asked. "I mean, Shepard isn't exactly Marilyn Monroe, but she isn't... I'll stop talking now."

"I'm here to ask for your help." Shepard continued, ignoring the Doctor.

"You show up in a Cerberus frigate to take me away somewhere?" Jack looked over the Normandy. "You think I'm stupid?"

"This ship is going down in flames. I've got the only boat off. I'm offering to take you with me, and _you're arguing._ "

"We could just knock her out and take her." Miranda suggested.

"I'd like to see you try." Jack returned.

"We're not going to attack her." Shepard said.

"Good move. Look you want me to come with you? Make it worth my while." Jack approached.

"Fine, I'll do what I can." Shepard sighed, getting tired of having to jump through hoops all the time.

"Don't make promises you can't keep. I bet your ship's got lots of Cerberus databases. I want in, see what they've got on me. You want me on your team, you give me that."

"Done."

"Shepard, you're not authorized to do that!" Miranda interjected.

"It pisses off the cheerleader." Jack grinned. "Even better. You'd better be straight-up with me."

Shepard just nodded.

"Then why the hell are we standing around here?" Jack asked.

"Move out." Shepard ordered, and the four boarded the Normandy.


	15. A Field Trip

"Hello, Susan!" The Doctor yelled, hanging upside down from the level above. They were in the TARDIS console room, just lounging around.

"Eek!" Susan shouted in surprise. "Grandfather, why are you hanging upside down like that?" She asked once the surprise subsided.

"Well, I can't every well talk and keep eye contact while being right-side up up here, now can I? Come on, we're going on a field trip!" He said, pulling himself up.

"A field trip? Where?" Susan asked, walking up the stairs to the console

"Earth!" The Doctor responded, setting the controls. "Specifically, Philedelphia, on July 4th 1776."

"What happens on that particular date?" Susan tilted her head.

"The signing of the Declaration of Independence, the biggest turning point in American history!" The Doctor pulled the dematerialization lever, and the TARDIS set off. "To think, that only thirteen wimpy colonies could come together and not only declare independence, but also fight for it against one of the biggest military forces that the world had to offer, and win? And then go on to become one of the most powerful nations on Earth? It is, quite frankly, inspiring. That is of course, if we're not also talking about the Corellian Revolution. Started that one myself, actually. That's what happens when you go visit a species that can only communicate in limb movements, and happen to have eighteen less joints then them."

"But why America?" Susan wondered.

"Would you rather go to the French Revolution, and risk being beheaded?"

"...I see your point. But still, grandfather, why?"

The Doctor rubbed his forehead. "You'll need to learn basic human history if you want to blend in, and I've learned to stay away from England. Especially in the past. Trouble seems to follow, otherwise."

"You? Trouble?" Susan scoffed. "Grandfather. you're one of the most non-troublemaker-ish people I know!"

"You don't know what I've been getting up to in the past nine-hundred years since I've seen you. Have I told you about the time I married Queen Elizabeth?" The Doctor smiled wryly.

The TARDIS engines wheezed, and finally thumped as the ship landed. The Doctor moved over to open the door, but was stopped by Susan, asking:

"Grandfather, shouldn't we change before we go out there?"

The Doctor frowned, confused. "Why would we do that?"

"So we blend in, perhaps?"

"Oh, yes, quite right." The Doctor nodded. "There should be clothes in the wardrobe. Off you pop. And don't take too long!" He shouted as Susan ran to the wardrobe. Minutes later, she came back, wearing period-appropriate dress.

The Doctor threw open the doors, and they stepped out.

"Wait a minute..." The Doctor looked around. "This isn't Philiadelphia, this is Boston!" He groaned in frustration. "I overshot... _again._ " But then, he perked up. "Then again, this _is_ where Paul Revere began his legendary ride..."

"Who and what?"

"Right, forgot you aren't that well-versed in Earth history. See, on April 18th, 1775 a man named Paul Revere, along a few other splendid chaps, myself among them, rode all the way from here to Concord with the goal of warning the people that the British army was on its way. But he never made it, and was instead stopped in a town called Lexington by British patrols."

"And what makes this ride of his so legendary?"

"Honestly? I don't know. Maybe it's how he was so determined. Maybe it's how it led America to winning the war. Or maybe, it's because the whole time, he kept yelling-"

"The British are coming! The British are coming!" A masculine American yelled, riding up behind them. He stopped, and dismounted his horse. "Sorry, I've always wanted to say that." He said, pulling down the hood on his cloak. "Hey, Doc." Jack Harkness smiled.

"Jack!" The Doctor smiled. "What are you doing here?"

"That's sort of a long story, but never mind that. Who's your new companion?" Jack winked in Susan's direction, causing the gallifreyan to blush.

"No, stop that!" The Doctor madly gesticulated. "You're married! And even if you weren't, she's my granddaughter!"

"Really?" Jack asked, eyes widening. "Other You's gonna wanna see this. Come on." Jack said, leading Susan and the Doctor back the way he came.

"What about the horse?" Susan asked.

"Oh, don't worry. He's fine where he is." Jack dismissed. He led them through the empty streets of Boston, to a small tavern-slash-inn on the edge of town. Jack took the two up the stairs, and to the room at the end of the hall. "Guys, we got guests!" He shouted, throwing the door open.

"Hold on, we just saw you." Rose said, looking at the Doctor. "It was on the Col-"

"Rose, _spoilers!"_ Jack emphasized as they entered entered. "That hasn't happened for him yet."

"Doctor." The proper Doctor said to the metacrisis.

"Doctor." He returned. Ten then looked at the other person that entered. "Susan." He smiled.

"Sorry, grandfather, who's this?" Susan asked, causing the Metacrisis's face to fall slightly.

"He's... me. Sort of. It's hard to explain." The Doctor answered.

"Technically, he's your uncle." Rose piped up again from where she and Sarah Jane were, looking over a map. "It's a long story, involving the almost-destruction of the universe, stolen planets, and a temp from Chiswick."

"What are you four doing?" The Doctor questioned.

"We're looking for a crashed spaceship." Sarah Jane answered.

"A _Zygon_ ship." Ten elaborated.

The Doctor nodded, and walked over to the map. "Well, that's rubbish, isn't it? The TARDIS could find that ship in seconds."

"There's a problem with that." Jack said. "The TARDIS got carried off, back to that ship. Hence why we're using conventional maps."

"What about the sonic?" The Doctor asked.

The metacrisis shook his head. "Can't. That ship may be crashed, but it's cloaked. Not even the sonic can pick it up. But the question should not be where they are, but what they're planning."

"I'll bite, what are they planning?" The Doctor asked.

"We don't know." Sarah Jane admitted, still studying the map.

Ten nodded in agreement. "This is our eighteenth consecutive trip in the new TARDIS. Only reason we're here is because the TARDIS just dropped out of the vortex mid-flight. So whatever they're planning, has to do with altering history. Then again, it usually does with these cases..."

The Doctor rubbed his chin in thought. "Jack has his vortex manipulator. He can use it to trace the temporal distortions back to their source."

"Don't you think we've already tried that?" Jack asked. "The distortions that ship's giving off messed with the vortex manipulator, activated the damned thing, and shot me right out of this era. Twice. First time, I ended up in ancient Egypt and ended up having a run-in with King Tut, horrible experience. The second time, I overshot completely. I only managed to get back with a lot of luck. That, and with a new control circuit I managed to pick up from a junkyard in the 6200s." The ex-Time Agent shrugged. "And that's not even mentioning the dimensional lesions."

"So, it seems that the distortions attract TARDISes, but repel vortex manipulators." Susan noted. "That can tell us a lot of how they plan to alter the timeline."

"That's just what I was thinking." Ten nodded. "Jack?"

Jack unstrapped the vortex manipulator, and handed it to his Doctor.

The metacrisis ran his own sonic screwdriver(a duplicate of Nine and the actual Ten's) over the manipulator's control panel, and held it up to his ear as it whirred. "Oh, that is most definitely not good..."

"What is it?" Rose asked, seeing Ten's worried look. "What?"

"I think..." Ten swallowed. "I think the Zygons have created a paradox."

"Hold on, if they did that, we'd know." Rose frowned.

"Rose, you know how people associate changes in time with ripples?" The Doctor asked.

"Yeah."

"Well, it's nothing like that, but if it works for you, go ahead." The Doctor said. "See, ripples, no matter how big or small, always go both ways. Or sometimes, all ways, into parallel universes and the like. Now normally, the ripples only go back a few days at most. But a paradox, like the grandfather paradox for example, happening is such a monumentally pants-browning moment on the cosmic scale, that it can ripple back months, or even years before the paradox itself actually happens. That's the distortions the VM was picking up."

"But then why has the TARDIS brought us here?" Sarah Jane asked.

"All TARDISes have base programming, no matter the model. If a TARDIS detects a temporal paradox, then it automatically lands close to it, and will not leave until time is put back on the proper course." The Doctor explained, clapping his hands together. "So! We need to find out what the paradox is, and get time back on track. Come along, everyone!" The Doctor said, dragging who he could along with him.

"Where are we going?" Rose asked.

"Back to my TARDIS." The Doctor answered. "We can use her to find the fixed point. And then, the Zygon ship. If its cloak isn't too advanced."

The six hiked through town, back to the original TARDIS, chatting it up while they did so.

"So... You're his granddaughter." Rose prompted Susan.

"Yes, I am." Susan responded. "Why?"

"The Doctor, the one that I'm used to, he's always saying that Time Lords didn't have families like the other species in the universe."

"We don't." Susan confirmed. "At least, not after the looms were invented."

"The what?" Sarah Jane's eyebrow skyrocketed, as she had been listening in somewhat.

"The last Pythia imposed a highly virulent sterility plague on the people of Gallifrey. I was actually the last child born biologically because of this. So to make sure that the gallifreyan species didn't go extinct, they divided people up into groups based off similar genetic characteristics, and put them all into houses. Then, each house was given a device called a loom. The loom would take a tissue sample, extract the DNA from it, and then break it down into its base proteins. Then, the loom would reassemble the DNA, but in a new configuration. After that, it would insert the DNA back into the tissue sample, and accelerate its growth, until a new, genetically distinct baby was formed. And then, the baby would grow like a normal gallifreyan."

"Hey, they have something like that in the 61st century!" Jack piped up from ahead.

"So what house was the Doctor from?" Sarah Jane wondered.

"We're from the House of Lungbarrow." Susan answered.

"Why did you two leave?" Rose wondered.

"The same reason as you. Well, not quite. After grandfather jumped into the loom, I had no other family left, so when he came back, I had no one to make me stay."

"Same reason as me? Did he tell you about me?" Rose asked.

"No. The TARDIS showed me files of every traveling companion he's taken on."

"He has files on us?"

"No." Susan repeated. "But the TARDIS does."

"Right-o, here we are!" Ten shouted, pushing open the TARDIS doors.

"Mister Harkness," Susan addressed, "you mentioned something about dimensional lesions?"

"That I did." Jack nodded.

"Grandfather, do you have anything that could help with that?"

"Hmm?" The Doctor looked up from the oval-shaped map unit set into the console. "Oh, right, right. There should be a dimensional equalizer in storage room seven, and enough components to build two spares. Let's see, if we overlay the map of the recorded temporal distortion patterns..." The Doctor mumbled, looking back down.

Susan nodded, and turned to Rose and Sarah Jane. "Come on, it's this way." She said, leading them off into the depths of the TARDIS.

Ten, with his brainy specs on, frowned at the map unit. "Those distortion patterns make no sense. And I have to say, planning things out like this and being careful really isn't like us." Ten commented.

"No, it isn't. But I've got Susan to think about, and if I lose her like I lost the Ponds... I don't know what I'd do." The Doctor quietly responded. "Jack, did your vortex manipulator also happen to record the locations of the dimensional lesions?"

"Yeah..." Jack said slowly. "Why?"

"Gimmie." The Doctor pulled the device off Jack's arm, and linked it to the TARDIS. "Bingo!" He said, as red dots were overlaid over the temporal distortions, causing something to be realized. "They're radiating inward counterclockwise in a spiral pattern, but if you look at that..."

"All of them except the center one are no smaller than a pinprick, but dimensional energy is flowing from one lesion to the other, like a bit of cable." Ten squinted. "It looks like all those other lesions are natural..." He then realized something. "The center lesion, that's where the Zygon ship is!"

"How can you be sure?" Jack asked.

"The dimensional energy is flowing from one to the other, all into the center, keeping it stable." Ten explained. "But the amount of energy required to open the lesion in the first place couldn't have been generated by anything in this time period. And the Zygons wouldn't have been able to open it a few meters away from their ship at the most."

"So that center breach is where the Zygons are." Jack nodded in understanding.

"Correctomundo!" Ten then acted like he had a bad taste in his mouth. "I swore to myself I'd never say that again."

"Right, I've already set the controls." The Doctor said, pushing the last button. "Shall we?" He pulled the lever, and the TARDIS demateralized.


	16. The Zygons' Master Plan

The TARDIS rematerialized, and the six gingerly stepped out into a dark cavern.

"Where are we?" Sarah Jane whispered.

"We're in an underwater cave at least a hundred miles away." The Doctor answered. "The biggest dimensional lesion should be nearby. You three have the equipment to close it?"

Rose, Sarah Jane, and Susan nodded, holding their dimensional equalizers.

"Good. Now, remember not to close the lesion until we figure out what they're plotting. Got that?"

The three nodded, and the six descended into the cave. They walked for at least half an hour, before coming to a dead-end, with a wall made by a firm-yet-soft meat-like substance causing the problem.

"Yep, that's definitely the crashed ship." Ten said, examining it.

"How can you tell?" Rose asked.

"Zygon technology is mostly biological, and that extends to their spaceships. Don't ask me how it works, 'cause I don't know."

"Now, how are we going to get in...?" Jack wondered.

"We could just knock." The Doctor said.

Everyone looked at him like he was the stupidest person in the cosmos. "What? It was just a suggestion." He pouted.

"You know, he might be on to something." Ten said after a moment. He started rapping his knuckles on the door in various places, until he hit a spot softer than all the others, and the door slid open. "Ah ha!"

The Doctor just looked smug.

The others (except for Ten) shook their heads, and entered. They came to a junction in the corridor, and it split off into three directions.

"Alright, we'll split up into groups of two." The Doctor started pointing. "Rose, you go with Jack. Sarah Jane, with me. And Susan'll go with... that one."

"Oi! That one!?"

"What exactly are we looking for?" Sarah Jane questioned. "And what are we supposed to do when we find it?"

"Like I said, the bridge, or wherever they're keeping the lesion. As for what to do..."The Doctor thought about it, and then pulled a gun-like object out of his pocket. He slid something into the top, pressed the barrel against his palm, and pulled the trigger. "Ow." He shook his hand. "These," He said, holding up his palm to reveal a slight bump, "are nanocommunicators. They link to the nerves in your hand, and transmit thoughts telepathically. Used something a little bit like this a while back, actually. Except they were recording devices, not communicators. Anyway, you press the bump on your palm, and it starts transmitting. We should be able to receive each other, no matter the distance. Now," He cocked the 'gun,' "everyone hold out your hand."

They all held out their left hand, and the Doctor went around, injecting the nanocommunicators into each.

"Alright, that should be all of you." The Doctor put the injector away. "Alright, gang, let's split up!" He chuckled lightly. "I've always wanted to say that. Well, I've always wanted to say a lot of things, that just happened to be at the top of the list this week." He rambled as he and Sarah Jane took the middle path.

The others followed their example, and took the left corridor and the one on the right.

* * *

"You're very confusing." Susan bluntly said to Ten.

"Oh?" His eyebrow arched.

"You feel like grandfather, and yet you don't at the same time." Susan said, sending that bit along telepathically to indicate what she meant. "I've only gotten a feeling like that from one other person."

"Who?"

"Commander Shepard. But she's... a lot more confusing. I mostly keep inside the TARDIS, but I can still feel her. And at times, Shepard just disappears for a few moments, and is replaced with grandfather. Yet, I can still feel him, running around acting insane."

"Yeah, she's a bit of a case, that one." Ten agreed. "I just came from a meeting with her, actually. I noticed that His emotional state tends to affect her just a little bit.'"

"Who's?"

"Correct." Ten grinned. His face fell when he realized something important. "You know what? I don't think I've spotted a single Zygon since we entered."

"I wonder why that is."

"Me too. But, if we find the bridge, we can do a scan for life-signs."

"Then I guess we had better go do that."

The two walked for another minute or so, before coming to a large, square pyramid-shaped chamber. The chamber was empty, but held a large sphere in the center, with monitors surrounding it.

"Is this it?" Susan asked.

"No, I think it's the reactor." He put on his brainy specs, and moved to inspect the monitors. His eyebrows skyrocketed, and he sharply inhaled.

"What is it?"

"This reactor is literally a miniature star, if it goes up it would take out everything from here to Jupiter!"

"Why do they need that much energy?"

"I don't know..." He frowned. "But it all seems to be going to the room at the end of the corridor Rose and Jack went down."

Then, vents started hissing, and a purple gas started filling the room, knocking out Ten and Susan.

* * *

"You know, this kind of reminds me of our wedding night." Jack smiled as the two of them walked. "Just the two of us, running around in a dark corridor, with no one to witness anything..."

"Stop it." Rose groaned.

"I was tempted to ask that Zygon to stay..."

"Jack, seriously. I'm trying to do what the Doctor said, and I can't if you're in my ear rambling on about your perverted twin-fantasies."

"Come on." He crossed his arms. "Don't tell me you didn't think about it too."

Rose tried to argue, but no sound came out, as she realized he was somewhat right.

She would never let him know that, though. She would never hear the end of it.

"Here's a question: Where is everyone?" She changed the subject.

"Out for a drink?" He shrugged. "This is a very small ship, relatively speaking. I wouldn't be surprised if it was only maintained by five of them, at the most. That, or it could be abandoned. After all, we haven't seen any actual Zygons. For all we know, the TARDIS could've just been carried off by one of the natives." The door at the end of the corridor opened, and they stepped in. "Oh my God..." Jack looked at the machine in the room.

"What is it?"

"It's a teleport." Jack said, looking at the distinctly cannon-shaped device, with very ornate writings on it. "It's a Time Lord teleport."

Then, a hissing sound started filling their ears, and purple gas started emanating from the small vents.

"The door!" Jack shouted, as he and Rose tried to escape.

But the door slid closed before they could get to it, the mysterious gas filled the room, and they blacked out.

* * *

"Here we are." The Doctor commented, as they came to a door. The door slid open, revealing a room filled with computer banks. "That can't be right..."

"What is it?"

"All of the corridors were the same length." The Doctor explained. "Meaning that we got in here as they did. Meaning that they haven't found the bridge."

"But there were only three corridors!"

"Exactly." Then, the Time Lord's eyes widened. "It's a trap!" He yelled, as the door shut, and the knockout gas filled the room.

He awoke several hours later in a small room, tied down to a chair.

"Ah, hello, Doctor." The Zygon across from him spoke.

"Oh, and who are you?" The Doctor responded.

"I am General Darmok." The Zygon sneered. "Of the-"

"Yeah, that's great and all, but where are my friends?"

"Your companions have been detained. They are watching us as we speak."

"Oh, so this is one of your gloating things, isn't it? How did you capture us?"

"We had you trapped the moment your TARDIS landed outside Ark Base."

"Ah, so it was a base, not a ship. That explains it. Why do you have a base set up, though?"

"Ark Base has three components vital to our plan." Darmok started pacing. "A Gallifreyan teleport, a micro-star reactor, and a Zaxton M-511 computer. These components are far too dangerous to store on a ship."

"Where did you get them?"

"We 'borrowed' them. They are essential to our plans."

"Plan?" The Doctor started thinking to himself. Zaxton computing was almost universally renowned for making very powerful computers, capable of simulating entire planets down to the subatomic level. Gallifreyan teleports could transport entire continents at maximum power. And the Micro-Star reactor was essentially just a souped-up fusion reactor, capable of generating enough power at once to power an entire planet. So whatever the Zygons were planning, it was big. "Well, enough beating around the bush. Ooh, I should use that more often... What's your plan?"

"As you know doubt remember, our homeworld, Zygor, was destroyed in the early days of the Time War to prevent the Daleks from using us as spies."

"So that's what this is all about... Another one of your schemes to make Earth into New Zygor."

"Correct, Doctor. And with the technology provided to us, coupled with the dimensional lesion reaching across time, it will be a simple matter of teleporting the population of Zygor to Earth."

"And what are you going to do with the human race?"

"Zygor was completely atomized, so it is very unlikely the Time Lords would notice the difference between the atoms that make up human and Zygon biology..."

"Are you insane!? You'd cause time to unravel like a cheap dishrag in the wash cycle!"

"Our Benefactor would beg to disagree." Darmok stressed. "Now, if you will excuse me, I must attend to the upcoming festivities." And then, he walked out.

The Doctor tried reaching for his screwdriver after Darmok left, but couldn't find it. It seemed the Zygons had confiscated it. But all hope wasn't lost, for as he reached into his pockets, he felt the small bauble-shaped bombs used by the roboforms being controlled by the Racnoss Queen. He pulled one out, and felt around for the remote control. He found it, and pulled it out.

Then, he activated the remote, causing the bauble to start hovering. He pressed one of buttons, and the bauble was sent flying into the wall, making a small explosion, and scattering bits of shrapnel in the room.

After the small wisps of smoke cleared, the Doctor reached for a bit of shrapnel sharp enough to cut through his bindings, and set to work.

* * *

"Ah-ha! Got it!" The Doctor shouted in triumph, as he broke free of his bindings. He jumped up from his seat, and looked around. He started looking around for something that could help him escape.

The explosive baubles likely weren't strong enough to blast through the door, and given that he didn't have the sonic, he couldn't hack it open.

But, he didn't need to, as Jack ran in.

"How did you get it unlocked?" He asked, slightly amazed.

"Wasn't locked to begin with." Jack said. "Come on. The other you should be-"

*BOOM!*

"-making a distraction." Jack meeky finished.

"Ha, excellent!" He shouted as they ran through the base's corridors. "How'd you lot get out?" The Doctor asked, as he and Jack rejoined the others, minus Ten. They were all standing outside a perfect recreation of the Tenth Doctor's TARDIS, in a room filled with terminals.

"They didn't take away his sonic." Rose explained. "They didn't think he was you, so they didn't search him."

"Well that was fortunate." The Doctor commented. "What are you lot trying to do?"

"We're _trying_ to stop the teleport's activation sequence." Susan said, as she and Sarah Jane were frantically pressing the controls on the terminals in front of them. "But it's not working!"

"Hence why the other you had to go off and make some trouble in the reactor." Jack explained.

 _"Alert: Prepare for teleport in five minutes."_ The voice of the Zygon computer announced.

"Well, that's my cue." The Doctor said, hopping into action. He charged over to one of the control terminals, and his fingers started flying over the keys. "It looks like that the teleport is hooked up to the main reactor only, and not any of the backups... Susan, do you know how to fly a TARDIS?"

"I'm good at flying the type 30s they used in the Academy," Susan shook her head, "but other than that..."

"Well, the old girl's Type 40 control scheme isn't do different." The Doctor encouraged. "I'm going to go do something incredibly dangerous, and will probably need a quick escape. Just go in, and wait for my signal."

"What signal?" Susan asked as she and the others piled into the TARDIS.

"You'll know it when you see it." The Doctor said, leaving the room.

Susan just shook her head, and closed the doors.

The Doctor was walking down to the end of the corridor, passing the cell he was in a moment ago. On the outside wall of the cell, there was a small compartment. The Doctor peeked inside, and brightened as he saw his sonic screwdriver. He grabbed it, stashed it, and proceeded into the end of the corridor.

He came to a circular dead end, and looked around. Seeing a glowing switch, he pressed it, and the floor under him started rising up, as the ceiling above him opened up. The elevator stopped in the same corridor junction that he and the others had been in moments ago. However, the entire place was now lit up, allowing him to see the clearly-labeled corridors.

He ran down the one marked 'Reactor' and entered, to see the Zygons standing over the knocked out Ten.

"It is too late, Doctor." The Zygon leader said. "You cannot stop the teleport."

"Except there won't be a teleport." The Doctor rebutted. "But there wasn't _really_ gonna be a teleport in the first place."

"You are wrong. The human race will perish."

"No, they won't." The Doctor argued. "'Cause that teleport you've got in there? I saw a glimpse of it on my way here, and that's nothing more than a bunch of bells and whistles hooked up to look like a Time Lord teleport. This reactor though, this is the real deal. And you know what all that energy you've got pumping into the shoddy teleport's gonna do? Overload. Everything in this base, along with the base itself, will be vaporized."

"Then you will help us."

"I most certainly will not!"

"Then the human race will die."

"No, they won't. Cause you see, this base is miles and miles away from any sort of civilization. And that reactor, even if it is the real deal, is one of the lower-end models. If it were to go up, even with the safeties off, most amount of damage you would cause would be to the little fish, swimming around without a care in the world."

"Then you shall die with us."

"No, you see, I don't think so." The Doctor stood directly over Ten.

"And why do you think that?"

"Because of this." The Doctor held up his sonic screwdriver, and pressed the button, causing the reactor core safeties to immediately be disabled, and accelerating the core meltdown. Then, the reactor room was gradually replaced with the other TARDIS's console room, as the ship made its iconic sound.

"Doctor!" Sarah Jane shouted as she ran to check on him. "Jack, help me get him to the sickbay!"

Jack nodded, and he and Sarah Jane carried him off, while the Doctor tended to the controls.

The TARDIS started landing again, and the Doctor ran to the door.

"Where are you going?" Rose asked.

"To fly my TARDIS up to the surface." The Doctor explained. "Susan, you fly this one up!" He ran out, and into the proper TARDIS, setting the controls.

Behind him, Ten's TARDIS took off, and soon, the Doctor's TARDIS followed.

Both TARDISes landed on a beach, looking out on the ocean. The Doctor ran out of his TARDIS, and the others (minus Saah Jane and Ten) out of the other one. A bright flash illuminated part of the ocean in front of them, and the ground shook beneath them.

"Well, there goes the Zygons." Jack remarked.

"Not entirely." The Doctor said. He walked over to his TARDIS, and pulled open the little telephone door, picking up the phone off the hook. He dialed the number, and started talking to someone, giving coordinates and the like. He then hung up, and turned back to the group."The Shadow Proclamation's on their way."

"Fat lot of good that'll do the Zygons." Rose said.

"No, they're on their way in the past. They'll teleport the Zygons away immediately after we leave the base." The Doctor clapped his hands together. "So, the human race is saved! Again!"

"Again?" Susan asked.

"Yeah, this sort of thing tends to happen a lot." Rose explained.

The Doctor looked down at his watch, and said. "Well, me and Susan have to be off. Shepard isn't going to be too happy if we show up late. Goodbye, you two." The Doctor said, running into the TARDIS.

"Goodbye!" Susan said, as the Doctor pulled her in.

The doors slammed, and the TARDIS dematerialized, leaving the other TARDIS, and Rose and Jack behind...

* * *

"Well, the day is saved!" The Doctor danced around the console.

"Grandfather, what did the Zygons mean by that?" Susan asked quietly from the top of the stairs.

"Mean by what?" The Doctor kept a cheerful facade, even though his hearts started to sink.

"The Time Lords, burning the Zygon homeworld." Susan continued, almost as quiet as a church mouse.

The Doctor sighed sadly, knowing that somehow a question related to the Time War would be asked. He walked up the stairs, motioned for Susan to move over just a bit, and sat down next to her. "There was a war. A Time War." The Doctor quietly told her. "The Time Lords fought a species called the Daleks, and the fate of the universe was literally at stake. In the early days, the Time Lords wanted the war to be a short conflict, so they started destroying any species that would ally with the Daleks, and the Zygons were among them. But, the conflict was anything but, and the war lasted for centuries, with no end in sight. But, eventually, it did end, four-hundred years later. But both sides were completely destroyed."

Tears started to flow from Susan's eyes. "But..." And then, she started to break down.

The Doctor then hugged Susan close, comforting her as she cried over her fallen people.


	17. Horizon

After Susan had stopped crying, the Doctor got up from his place at the top of the stairs, and walked down to the console, activating the controls that would land the TARDIS. After the TARDIS finished materializing, a loud banging came from the doors.

"Doctor!" Shepard shouted. "We need you!"

The Doctor flicked a little toggle switch on the console, and unlocked the doors, allowing Shepard to come sprinting in, clad in her armor. "What's all the racket about?" The Doctor asked.

"Okay, never minding the fact that you disappeared for about a week without a trace, we've got trouble." Shepard said.

"What kind of trouble?" The Doctor inquired.

"Another one of our colonies is under attack, _right now._ " Shepard said. "We've got a countermeasure for the seeker swarms, but no idea if it's gonna work or not."

"So you want me to come down? Make sure it works right?" The Doctor guessed.

Shepard nodded, confirming his guess. "I would ask Mordin to do it, but he had an accident in the lab. He's in the medbay, knocked out, which means that you're the only one with the knowledge of how the countermeasure works, and how to fix it if it goes wrong."

"Lucky me." The Doctor scoffed sarcastically. He then turned to Susan, who was still sniffling some. "I'm going to go out for a while." He quietly told her. "While I am, I want you to go out and socialize with the crew of the Normandy for a bit. It'll do you good to get out of the TARDIS for a while. Hey," He then got to eye level with Susan, "Everything is going to be _fine_. I promise." He straightened back up, and walked over to Shepard. "Let's go."

Shepard nodded, and they walked through the doors. "What'd you do?" She angrily demanded after the doors shut behind them and locked.

The Doctor's eyebrow sharply raised. "I don't see why you should care. She's _my_ granddaughter, not yours."

"Whether she is my granddaughter or not, you did something to make an innocent fift- er, two-hundred year old cry." Shepard retorted as they met with the others, and boarded the shuttle. "Anyone who cared even a little bit would be a little angry." She said, as she and the Doctor sat down. The shuttle was packed with the current members of the suicide squad that Shepard had built up. Jack, Miranda, Zaeed, Kasumi, Garrus, Grunt, and Jacob were all packed together like sardines.

The Doctor raised his eyebrow at the towering alien.

"What're you looking at." Grunt boomed.

"He's our latest recruit." Shepard told the Doctor. "A lot happened in that week you were gone. By the way, we're going to have a talk about doing that when we get back to the ship."

"I wouldn't expect otherwise." The Doctor smiled. He clapped his hands together, and started asking questions. "So, anything I need to know about this colony?"

"Not really, no." Shepard shook her head. "It's just a normal colony."

"Commander, we'll be hitting the LZ in five!" The Cerberus pilot reported.

Shepard nodded, and the group prepared for the fight.

* * *

Susan absentmindedly wandered through the corridors of the Normandy. So far, at most of the areas of the ship she had visited, she was turned away because they were currently on high-alert, meaning non-essential personnel weren't allowed in critical areas.

Which, so far, was proving to be unfortunate for Susan. She had been trying to focus her attention to something else, anything but the destruction of her people.

She got her wish, when she noticed the Salarian scientist in the medbay. If no one else was willing to talk with her, maybe he was.

"Ah," Mordin inhaled as he saw Susan enter, "Doctor's granddaughter. Susan, I believe?"

Susan nodded in lieu of a verbal response, and looked at Mordin's injuries from where she stood. The Salarian had burns -not too severe- covering half of his face, and a deep cut on his forehead. "What happened?" Susan curiously asked.

"Equipment overload." Mordin answered at his usual fast-pace. "Was analyzing genetic sample, scanners could not handle work-" He inhaled, "-exploded. Don't worry, looks worse than it feels." Mordin tried to smile, but it turned into a grimace of great pain.

"Here, let me help." Susan said, approaching. Her hands started to emit golden energy, and she touched one of her fingers to the burned area of Mordin's flesh. Instantly, the same energy covered Mordin, and once it died down, he emerged.

Mordin looked twenty years younger, which for a Salarian, might as well have been sixty. The burns were healed, and the cut, and his other horn-thing had grown back.

Mordin's eyes widened as Susan pulled her hand back. "Interesting regenerative capabilities. Feel thirty years younger. Thank you."

"You're welcome." Susan returned. "Oh, and don't mention this to grandfather, will you? It wasn't a full regeneration, barely a fifth actually, but he'd still throw a fit if he knew I used it. So," She clasped her hands together, "What kind of genetic sample were you analyzing?"

Mordin sighed. "Commander Shepard's. Collected in secret, would not let her know until results of test came in."

"Why run the test in the first place?" Susan tilted her head.

"Discovered comprehensive medical data gathered from Doctor's physical. His internal physiology was remarkably similar to Shepard's." Mordin explained. "Human scientists deemed her 'defects' as results of experimentation, or advanced genetic engineering. STG also had data pertaining to Shepard's 'condition', most of it reviewed by myself, actually. Once I saw the Doctor's results, deemed them too similar to be coincidence."

"So you took a sample of blood, to try and compare her DNA to grandfather's." Susan understood. "But where would you get the other sample?"

"Doctor infected with plague back on Omega, started coughing up blood." Mordin said. "Managed to reclaim samples from clinic floor. Brought them with me when I boarded, but was afraid to run tests without more samples. But, once Shepard's uniqueness became apparent, had to run tests. Had to find truth. But lab equipment exploded before tests could complete."

"So, what did you learn?"

"Nothing." Mordin shook his head. "No data yield before scanners were destroyed."

"You know, the TARDIS has some equipment that you could use."

"TARDIS?"

"Come on, I'll show you."

* * *

The Doctor's tongue poked out of the side of his mouth as he looked intensely at the omni-tool he'd been given. "If I'm reading this right, and I honestly think I am, there's not a lot of seekers here, so Mordin's thingy should work." He reported as the others piled out of the shuttle.

"Good." Shepard said. "You stay in the center of the group. We can't have you die on us, you being the only one who knows how this works, and all."

The Doctor nodded, and the team set out, pushing their way through the town, and fighting the Collectors that moved to stop them. The fighting was standard-fare, the Collectors seemed to have two standard units, a drone-like footsoldier with no defenses beyond standard shields, and a tougher one with a biotic barrier and some ind of energy weapon. After they took them all out, the team proceeded, as the Collectors they had killed disintegrated.

They came to another small area, with husks and collectors loitering around. Shepard's group opened fire, and within a minute, combat was over.

"These look like the husks the geth used while I was hunting Saren." Shepard commented, looking down at the body. "Except different, more advanced."

"Just one more piece of evidence that pins the Collectors as servants to the Reapers." Miranda said.

"D'you think this is what they're using the abducted colonists for?" The Doctor asked, looking down at the husk, while anger bubbled up deep inside him.

"Maybe some, but not all of them." Shepard shook her head. "Husks aren't the most intelligent soldiers. The Collectors are using the colonists for something else, experiments maybe?"

"Maybe..." The Doctor's eyes narrowed. "But it doesn't matter. Whatever they're doing, they're going to be stopped."

"Couldn't have said it better myself." Shepard smiled. "Come on, the more we wait, the more time we give the Collectors to get out of here." And with that, the group pressed forward.

The group fought through more Collectors, and came to a block of prefabs. They came to a set of stairs, with a man at the bottom of them, frozen mid-running like a statue.

"Oh dear..." The Doctor mumbled as he examined the man. "He's still conscious." The Doctor stashed his screwdriver, and addressed the frozen man. "Don't worry, it should wear off in about an hour." The Doctor got back at the center of the group, and they proceeded, but not before Shepard picked up some kind of Collector weapon, and stashed it.

As they were proceeding, they could hear weapons fire in the distance.

"Looks like someone's putting up a fight." Shepard commented. "Come on, everyone! Double time!"

They came to an area in front of a large gun-like tower, where a woman with blonde curls and Indiana Jones-ish getup was fighting the Collectors single handedly.

 **"WE ARE HARBINGER."** A Collector boomed, as it hovered in the air, and underwent some kind of transformation. Its skin cracked and glowed an angry orange, as the Collector increased in strength ten-fold.

"River!?" The Doctor shouted, as he dove into cover next to her.

"Hello sweetie." River responded, as she peeked up to fire on Harbinger.

"What in God's name are you doing here!? _How_ did you get here!?"

"Sorry, sweetie, but I'm not _that_ River." She mildly condescended, as the others focused on Harbinger. "She's just letting me borrow her appearance for a while. And the catchphrases."

"So that means you've _met_ my River. The mind races..."

"Does it now?" River smiled.

"So, I'm going to guess we've already met. From your perspective, at least." The Doctor theorized.

"More than that, you made me what I am today." She said, popping back up and firing more energy pulses at Harbinger. "Can't say anymore. Spoilers, and all that. As for what I'm doing here, I was writing a book, and the historical records were a bit too vague, so I decided to go back and see it for myself. Very easy if you've got a time machine.. "

"Oh, that's good." The Doctor said, peeking out to try and use the sonic to disrupt Harbinger's barriers. "How much have you got done?"

"The first sixteen chapters." River answered. "But I still have the Reaper War to cover, so I'll probably end up splitting it into volumes."

"Good idea. Never could get into reading those really long books with almost a hundred chapters, myself."

"Doctor!" Shepard shouted. "Less flirting, more shooting!"

"How was that flirting!?" The Doctor stammered.

"With me in the vicinity, it's very hard to tell." River's mouth curled into a smile.

 **"YOU CANNOT STOP US, SHEPARD."** Harbinger boomed as the Collector it was possessing began to disintegrate. **"THIS FORM IS DISPOSABLE. WE WILL RETURN."**

Shepard holstered her pistol as the Collector turned into a cloud of ash. "Who's this?" She questioned, approaching River. "And how'd she not get taken?"

"Professor River Song." River smiled, as if seeing someone she hadn't seen in a long while. "As for that second one, I got here shortly after the attack."

"Professor?" Shepard's eyebrow raised. "What of?"

"Archaeology."

"Archaeology? We're going to have to introduce you to Liara someday..." Garrus commented.

"Um, in case you all forgot, the colony is still in the middle of _being attacked_." Miranda emphasized.

"Right." Shepard acknowledged. She then turned to River. "You wanna come with? We could always use a little extra firepower."

"Sure, why not." River shrugged. "I'm going to have to head back to the University after we're done, however." The group came to a large door, and Shepard moved to hack it, before River stepped forward. "Let me." River pulled a gun-like object from its holster, and aimed it at the door. She pulled the trigger, and a large square was projected onto the door, as the gun made a high-pitched whine. The square section of the wall disappeared, allowing them a method of entry.

"Showoff." Shepard mumbled.

* * *

Susan showed Mordin to the TARDIS, the Professor looking at it curiously as they approached. "Okay, you might want to prepare yourself for a little shock." Susan warned, unlocking the doors. She pushed both doors open, and stepped inside. Mordin followed, after a brief moment of hesitation.

"Incredible." Mordin breathed in awe, as he looked around the console room. "Interior dimensions entirely separate from exterior. How big?"

"The TARDIS weighs, on Earth, around fifty-thousand metric tonnes."

Mordin's eyes widened. "Weight would crush Normandy like ant under boot! Prevented... how?"

"That's the weight of the TARDIS's interior dimensions." Susan elaborated. "The exterior shell is just that-a shell. It weighs no more than an ordinary Police Box from Earth. In most circumstances."

"Would love to know more about workings, perhaps in future." Mordin said. "For now, must work on sample analysis. Where is lab?"

"This way." Susan guided Mordin through the door at the bottom of the console room.

They entered one of the TARDIS's many corridors, and took a right, coming to a hexagonal hole in the floor. Mordin raised an eyebrow, and Susan jumped down it, but instead of dropping like a rock, she floated down like a feather, landing gently on the level below. Mordin followed, and they turned around, going right once they came to another fork in the corridor. Eventually, they came to a hexagonal room, which emitted a green glow, and was filled with various lab equipment.

Mordin pulled the samples out of their carrying case, and set to work, as Susan looked on.

A few moments later, Mordin's eyes widened as he made a breakthrough.

* * *

The large door behind them closed as the group left the small bunker. They talked to a mechanic who had taken refuge inside, and were told about the GUARDIAN defense towers that had been installed by the Alliance.

So now, that's where they were heading. They came to a plaza swarming with Collectors, and they all took cover.

 **"ASSUMING DIRECT CONTROL."** Harbinger boomed from across the battlefield.

The smaller drones were the easiest to take out, going down with just a couple of shots. But Harbinger was a different story entirely.

 **"YOUR WEAPONS ARE USELESS. WE ARE UNSTOPPABLE."**

"Oh, there he goes." The Doctor groaned. "With the whole 'We are invincible' shtick."

 **"TIME LORD."** Harbinger addressed in response. **"YOUR PEOPLE ARE ARROGANT TO THE POINT OF STAGNATION. YOU ARE WEAK, JUST AS THEY."**

"Everyone stop firing!" The Doctor yelled, causing everyone to do just that, in confusion. He got up from cover, pointing the screwdriver directly at Harbinger as he did so. "I've figured out how you're possessing your subordinates, how to stop the signal in its tracks, and as an added bonus, how to keep you locked in that body until I want to let you go. So, start talking, or you can run the risk of being permanently damaged. Your choice..."

 **"YOUR THREATS ARE USELESS. WE ARE MANY, YOU ARE BUT ONE."**

"Yes, but if you know anything about the Time Lords, you know what we're capable of." The Doctor growled. "I could go back and ensure that your entire species never crawled out of the primordial muck. So, _talk."_

 **"WE HAVE HARVESTED MILLIONS OF SPECIES. YOURS IS SIMPLY ANOTHER FIGURE."** Harbinger then burst into flames, and turned to ash.

"Well, I wasn't expecting him to do that." The Doctor said, stashing the screwdriver.

"Come on, we have that tower online." She said, leading them through another large door, into a bigger plaza.

In the center of the plaza, an antenna was poking out of the ground, with a computer terminal attached to it. Shepard approached the terminal, and connected it to the Normandy's systems.

"Normandy," Shepard addressed, opening the commlink, "Do you read?"

 _"Joker here."_ The helmsman responded. _"Signal's weak, Commander, but we got you."_

"Alright, EDI get these defense towers online, yesterday."

 _"Errors in the calibration software are easily rectified, but it will take time to bring the generators to full power."_ EDI warned. _"I recommend a defensive posture. I will not be able to masked the increased output."_

"Great, we'll be surrounded on all sides, under fire constantly." Shepard groaned. "Any other helpful tips?"

 _"Just one: The Collectors are approaching your position. I recommend you ready weapons."_

"Doctor, you good with computers?" Shepard requested.

"Sure." The Time Lord shrugged.

"Do what you can to help EDI." Shepard ordered. "The rest of us will keep the Collectors occupied."

The Doctor nodded in acknowledgement, and approached the terminal, going over it with the sonic, as the Collector forces started dropping out of the sky.

"Well, that's rubbish." The Doctor mumbled as the gunfire rang from behind him. "They're never going to get those lasers online at this rate. Let's see, reactor control, reactor control... Bingo!" The Doctor's fingers started flying over the holographic keypad, and the Doctor routed a small jolt of energy from the secondary generators, the the primary ones, jumpstarting them, and causing the time the lasers took to power up to cut in half.

The fighting had stopped, but not before a large behemoth flew out of the sky, and landed right next to the group.

"Everyone, focus your fire!" Shepard ordered.

But it wasn't working, the creature's powerful biotic barrier was absorbing the gunfire like it was nothing.

The Doctor frantically searched his screwdriver for a setting that could destroy the barrier, or at the very least, disrupt it. After a moment, he happened across setting 8879004326b, which was used to disrupt the flow of dark energy currents. He took aim, pressed the activator down, and the creature's barrier dispersed, allowing Shepard and co to do some serious damage.

After about a minute of sustained fire, in which the creature tried to scramble to safety, it crumbled to dust, making the area clear of Collectors.

"Look!" Jack shouted, pointing at the Collector ship.

EDI had already started to fire the defense cannons, as explosions hit the outside hull of the Collector ship. But the bottom of the ship was rotating, and reconfiguring.

The ship's engine lit, kicking dust and dirt into the air, as it took off, leaving the colony behind.

"No!" The mechaninc from earlier shouted, running into the square. "You can't just let them get away!"

"Do I look like I have a _fucking jetpack_ to you?" Shepard scowled.

"Half the colony's in there!" The mechanic continued. "They took Egan, and Sam, and-and Lilith! Do something!"

"Hey, you think I _like_ seeing those bastards get away?" Shepard angrily retorted. "I did what I could."

"Yeah." The Doctor agreed. "But it never gets easy, not being able to save everyone. Does it, Shepard?"

"Shepard? Wait... I know that name." The man turned around. "Sure, I remember you. You're some kind of big Alliance hero."

"Commander Shepard." Another man said, walking out from behind a couple of crates. "Captain of the Normandy. The first human spectre. Savior of the Citadel." He said in reverence. "You're in the presence of a legend, Delan. And a ghost."

"All the good people we lost, you get left behind." The mechanic shook his head. "Figures. Screw this, I'm done with you Alliance types." He then walked off.

Kaidan -if the Doctor remembered correctly- walked up to Shepard, and held out his hand. "I thought you were dead, Commander. We all did."

"It's been too long, Kaidan." Shepard shook his hand, smiling. "Hope the last two years have been treating you well."

"That all you have to say?" Kaidan gave a humorless chuckle. "You show up after two years, and act like nothing's happened? I would've followed you anywhere, Commander! We all would've. Why didn't you try to contact any of us? Even just to let us know you were alive?"

"If I may interject." The Doctor awkwardly said, approaching. "She's been... part of a deep-cover mission for the past two years, under the pretense of dealing with the Collector threat. Yeah, that sounds good." He mumbled that last sentence so quietly, that no one could hear it. "A single transmission could've given her away, risked the whole mission."

"Mission?" Kaidan incredulously repeated. "The mission where she's working for Cerberus?"

"Again, deep-cover. But of course, you don't believe me. So," He flashed the psychic paper. "Alliance ID." He put it into his other arm behind his back. "Council Credentials." He kept alternating. "Character references. And the mission objectives. Now, Staff Sergeant, what's going to happen is that we're going to walk away. You're either coming with us, to help us stop the real culprits, or we're going to go our separate ways. But either way, _you can't mention a single word of this to anyone._ Clear?"

"Clear enough." Kaidan stepped back. "I'm going back to the Citadel, let them see if they believe you. Goodbye, Commander." Kaidan said, walking off to the nearby spaceport.

"Joker, send the shuttle." Shepard ordered, activating the comm. "I want off this planet."

* * *

"Ow!" The Doctor yelled, as his face hit the shuttlebay's floor.. Above him, Shepard's fist was balled up. "What was that for!?"

"I have had it with you!" Shepard said, silently bristling with anger. "For the past... six weeks, I have put up with you going out on your flights of whimsy without asking first, disappearing for days on end, and just being a damn weirdo! And I've been doing well, I think. But today was the final straw! I had it under control with Kaidan, and you had no business butting in like that!"

"Yes, I did!" The Doctor retorted, pushing himself up off the floor. "If I didn't, that little reunion of yours would've devolved into a shout-off!"

"I had the situation under control!"

"No you really didn't!"

"And how did you come to that conclusion!?"

"Because you're me!" The Doctor yelled. Once he realized what he had spat out, all anger left his voice, and he calmed. "Assemble the team in the briefing room. I won't be but a moment."

"And why should I listen to you?"

"Because if you want answers, that's the only way I'm going to give them."


	18. Explainations

After Shepard went off to assemble the team, the Doctor found himself walking into the TARDIS, the timeship directing him to Susan, and though he didn't know it yet, Mordin.

He walked into the lab, and his eyebrows climbed into his hair. "Susan, care explaining why Mordin is in here?"

"Well, he needed equipment to analyze Shepard's blood, and none of the equipment on the Normandy would work." Susan explained quickly.

"Hmm. That works out perfectly for me, then." He then turned to the Salarian. "Shepard's assembling the team in the briefing room. Take your data, and go there. I might need it."

Mordin nodded, and went to do just that.

"Susan, did you do what I think you did?" He asked, voice low.

"Grandfather, he was hurt!" Susan retorted.

"He would've healed on his own."

"Yes, he would, but think about it! Now, he gets to live longer! Wouldn't you have done it too."

"Yes, I suppose I would've,, but that's not why I'm here... Listen, there's something I need to tell you." The Doctor led Susan back to the console room. He sat down on the stairs leading to the bottom level, and directed Susan to sit in a little chair across from him. "Susan... I'm not your grandfather."

"Don't be ridiculous. I know you are, I felt it!"

"I am the Time Lord that used to be the Other." The Doctor agreed. "But I'm not _your_ grandfather." He shook his head sadly, looking down at his feet. "I'm from another universe. And so's my TARDIS."

"Grandfather, if that were true for even a moment, then how is the TARDIS still alive?"

"I don't know." The Doctor admitted. "In my universe, the Time Lords erected a barrier, a wall of sorts, to keep the Time War from spilling out into other realities. I suppose that whatever happened that let me pass through it from my universe to this one, is also letting the TARDIS draw energy from it."

And it was at that moment, that Susan started to believe him. "But... why?"

"Everyone died in the war, Susan. Everyone." The Doctor started tearing up. "Including... Including _you_. Once I got the chance to see you again, even if you weren't strictly the Susan that _I_ knew... It was too good to pass up. I'll admit, I acted a little impulsively. But that doesn't make it okay. I lied to you. I'm not your grandfather. I'm not even sure your real grandfather -or grandmother, confusing that is- knows that she's your grandfather."

"But you are my grandfather." Susan tilted her head. "You may not be from this universe, but that doesn't change it."

"You're not angry? Not even sad?"

"I might be in a little while." Susan shrugged. "Given that you made me assume that everyone I knew and loved was dead, though that might not actually be the case. But for now, I'm fine." But something kept bugging her. "If you're not the grandfather that threw himself into the loom, then who is?"

"Crikey, I forgot about that." The Doctor said. He pushed himself up, and started typing something on the keyboard integrated into the console.

"What are you doing?"

"I'm linking the TARDIS's databanks to the Normandy's computers. Nothing much, just the Index Files. I'm going to want them on standby, just in case. Right," He clapped his hands together, "Let's get this farce over with."

* * *

 _Meanwhile..._

"...I just don't get it." Shepard shook her head. "He said, and I quote: 'Because you're me!' What's that supposed to mean?"

"Well, we don't know everything about his species, right?" Kelly Chambers, the ship's resident shrink, assumed. "Nothing about their society or customs?"

"Right. What little he gave Doc Chakwas was enough to prove he was alien."

"Maybe you're like his clone or something." Kelly suggested. "Your... conditions certainly look a lot like his internal scans. Maybe his people treat cloning differently?"

"Could be... But I think the truth is going to be a lot stranger." Shepard shook her head. It was at that moment, that the elevator door opened, and the Doctor and Susan walked out. "Good, you're here. Come on, the meeting room is this way." Shepard led the two through the science lab, and into the small room.

All of the current members of the team were gathered up around the table in the center of the room.

"Alright." Shepard said, crossing her arms. " _Explain._ "

"Right." The Doctor nodded. "The first thing that you should know, is that I am from a different universe. Coexisting on the same dimensional plane, but out of phase with this one. My people, the Time Lords of Gallifrey, perfected a way of travel through both space and time, called a TARDIS. Shepard can vouch for the TARDIS's existance personally. Three Time Lords worked on the power source required to power such a vessel- Rassilon, Omega, and a Time Lord known only as the Other, who would all eventually become revered like Gods. Rassilon eventually became Lord President of Gallifrey, Omega fell into a black hole, becoming trapped in an antimatter universe, and the Other just... vanished. And before you ask, no. I'm not giving _anyone_ free range of my TARDIS."

Miranda visibly deflated at that.

"Anyway, it turns out that the Other didn't just vanish. He technically committed a form of suicide. He threw himself into a loom -which is how we Time Lords reproduced, by the way- and was broken down to the microcellular level. But before he did, he promised his granddaughter, and I quote: 'One day, I shall come back. Yes, I shall come back. Until then, there must no regrets, no tears, and no anxieties. Just move forward in all your beliefs, and prove to me that I am not mistaken in mine.'"

"I... I remember that." Shepard said slowly, as her eyes widened. "Clear as day. How can I remember something that's never happened to me?"

"You'll find out. It'll come to you eventually, I promise. Gallifreyan society went on, with barely a feather ruffled, and even forgot about him as time passed."

Shepard seemed to be saddened. "A legendary figure just up and vanished, and no one really cared?" Subconsciously, something within her stirred.

"Sadly, yes. For all his contributions to the Time Lords, Rassilon struck the Other's name from every record, a declared it a maximum offense to even utter his name. As time passed, and the Time Lords became more and more advanced, they forgot about the Other, until those who believed he existed and Rassilon had stolen his credit were declared 'madmen' and 'cultists.' Eventually, the loom the Other had thrown himself into was reactivated, and a baby was created. A baby formed from the essence of the Other. A baby that would come to be known as Theta Sigma of Lungbarrow House. In my universe, Theta Sigma was loomed as a boy. But in this one, Theta was loomed as a girl. But in _my_ universe, Theta Sigma grew up normally, went to the Academy, and picked his new name."

"Picked a new name?" Garrus asked.

"Yes, after you graduate the Academy, you discard your Gallifreyan name, and pick the name you'll use as a Time Lord. Theta picked 'The Doctor.'"

"So... you're the Other?" Shepard asked, trying to make sure she understood.

"Yes. But no. I have all his memories, his experiences, what made the Other the Other lives on in me. But it's like a dream. Fuzzy in some places, broken, and I doubt that will ever be fixed. But that's over in my universe. Like I said, over here, I was loomed as a girl. I can only guess what happened after that, but... Shepard, do you still have that plaque that was left with you as a baby?"

"Yes..." Shepard pulled a gold necklace off, with the plaque attached to it. "It's my good-luck charm. Do you know how many times I nearly died before this thing came in handy? As an impromptu weapon, or tiny bulletproof shield? It's also the only thing that I kept with me when the original Normandy was destroyed."

The Doctor looked down at it. Sure enough, the plaque had tiny dents in it where the tiny metal shavings that were used as projectiles hit it, a few miniscule blood stains where it had been used as a melee weapon, and a few scorch marks from atmospheric reentry, making it readily apparent that the metal the plaque was made out of was not simple gold. "Shepard, have you ever took the time to read the wording on the plaque?"

"No." The Commander shook her head. "Why would I? There's none there."

"Yes, there is." The Doctor traced his fingers along the etchings. "You can't notice them, because they're being concealed by a perception filter. They only register subconsciously. You need to look, really examine every detail, before you can notice them."

He handed the Commander the plaque back, and she stared down at it, transfixed.

"I can't see anything."

"That's because you're just staring at it. Look. Really look."

She tilted her head, and started examining the plaque's every scrape, every dent, and every stain. Eventually, she noticed it. Faint words were etched into it, but they were almost ghostly and not quite there. As she focused on the etchings, they became more and more real, and 'solidified.' "It's just a bunch of circles. Why do I need to notice them?"

"The Gallifreyan language is a wondrous thing, by speaking Old High Gallifreyan, you could warp reality. But that's not what you should be focusing on. Turn the plaque around."

Shepard did just that, and nearly dropped it in shock. _'Theta Sigma, Lungbarrow House'_ was engraved in ornate cursive writings. "That can't be right... My name is Thea, not Theta!"

"It's just one T short. Even if you couldn't notice them directly, the markings would've still registered at the subconscious level to anyone who examined the plaque. Including your mother."

Shepard stared down at it in shock. "So that's what you meant... All those dreams and outbursts I've been having, they were...?"

"Those were probably just the Other trying to reassert himself after too long a nap." The Doctor nodded. "Happened to me too. During puberty. That was hell, let me tell you. His voice constantly saying 'Oh, she's nice looking, don't you think?' and 'I think she'd be a great bondmate for you, how about it?' Took all the strength I had to not beat my head against the wall in frustration."

"But what will happen to me?"

"Well, you're past puberty, so I don't think he'll be trying to play matchmaker. But his little 'visits' will start to become more frequent, and longer lasting, until one of two things happens. Your personality melds with his, and you get all of his memories and the like out of it, or he takes over, and it's 'Bye bye, Shepard.'"

"Well, is there anything you can do?"

"Maybe. All of this was triggered when you entered the TARDIS for the first time. The old girl probably thought those memories had been taken away forcibly, and decided to help you get them back. And then she lied to me, trying to keep the process running smoothly. I bet if we can get you inside, she can make the process run a whole lot more smoothly, maybe even accelerate it. And that's all I really have to offer. Mordin's got the results of a few DNA tests he ran, and I've linked the TARDIS databanks to the Normandy computers, so you can verify my claims anytime you want. Now if you'll excuse me, I've got an appointment with a bowl of custard, and fish fingers. Come along, Susan!" And the two left the room.

"Shepard, please tell me you were humoring him." Garrus said.

"Yeah, you don't seriously believe that guy, do you?" Kasumi asked.

"But I can see the text right here. Clear as day." Shepard argued.

"He wasn't lying." Zaeed shook his head.

"And how do you know that?" Jacob asked.

"We're good at reading people. He just had that air about him, you know?" Jack piped up. "He might be a crazy fuck, but he was telling the truth. Least, that's what he thought."

"Doctor telling truth." Mordin vouched. "Saw interior of TARDIS myself. Fascinating ship. Bigger on the inside!"

"There are all sorts of ways to make an illusion like that." Miranda shook her head.

"...You're all dismissed." Shepard said, walking over to the door. "I'll be in my cabin."

* * *

 _"...You're right. That is unbelievable."_ Hannah Shepard said, her face being projected where the model ships were normally situated.

 _"I always knew you were special, but this..."_ Anderson let it hang, as he was projected on the wall to Shepard's right. He shook his head, and chuckled. _"I always knew you were destined for greatness."_

"So, what happens to me now?" Shepard asked. "Do I get taken away to some lab to be experimented on?" She said ruefully. "Will the Council condemn me for being a Gallifreyan?"

 _"You know damn well that's not going to happen, hon."_ Hannah said. _"If they try, there'll be a witch hunt. As for what to do next, I searched long and hard for anything that would give us a hint as to who your biological parents were, and got nothing. Now, you've got a chance to find out. Take it. I'm sure the... other you, would be happy to lend a hand."_

 _"Also, you should take this opportunity to try and convince the Time Lords to help us."_ Anderson suggested. _"They had the power to destroy entire planets at the push of a button. If that isn't useful against the Reapers, I don't know what will be."_

 _"Just remember, you don't have to if you don't want to hunt your biological parents down, you don't have to. I've gotta go, but consider what I said. Goodbye, love you."_ And like that, the link cut out.

The picture of Anderson switched to where Hannah was a moment ago. _"Now with her gone, I can finally let you know without a total freak-out."_

"Tell me what?"

Anderson rubbed his forehead. _"Well, I managed to figure out how the others identified the Doctor. The Shadow Broker's got bugs all over your ship. From what I heard, they can't record audio, but they can record picture. And they got the footage of the TARDIS landing in the shuttlebay."_

"Well, damn." Shepard groaned. "I'm gonna have to do another sweep. But how would that make mom freak out?"

 _"It wouldn't. But this next part would. Ever since your visit, they've been getting more and more paranoid. Panicked, even. They think that the Time Lords are returning for a full-scale war. But that's not the worst of it. They've made it a standing order to execute any Time Lord, or an agent of theirs, on-sight. Do you know what this means?"_

"If they find out about my 'condition' they'll kill me no matter what I've done for them." Shepard shook her head. "What are we going to do?"

 _"As of right now, not a damn thing. It's like they're trying to discredit everyone you've ever come into contact with."_

Shepard just sat there, thinking. "You think they know?"

 _"It's certainly possible."_

"...Right then." Shepard got up. "I'll convince the Doctor to take me to Gallifrey. See if they can help us."

 _"You go do that. I'll keep trying to control this situation. Anderson out."_

It was at that moment, that the lock on Shepard's door beeped.

"Come in." Shepard ordered.

The door slid open, and the Doctor entered. "Listen, uhh..." He rubbed the back of his neck. "Sorry. About earlier. It's not exactly easy learning that you're an alien, is it?"

"Susan made you come up here, didn't she?"

"Yeah, kind of. So, how are you taking it?"

"You know, all things considered, kind of alright."

"Good, because we're going on a trip!"

"What kind of trip?" Shepard asked, a bit suspicious.

"A TARDIS trip!"

"Where?"

"To Gallifrey! Oh, don't look so surprised. I was listening in. Well, don't just stand there! Time's-a-wasting!"

"And what makes you so sure that I'm coming along?"

"You need help against the Reapers, and they can provide it. They might also be able to fix that little memory problem of yours."

"...Fine. Let's go." She reluctantly said, following him down to the TARDIS. "But we'd better be back as soon as we left."

"Your wish is my command."

The elevator crawled down to the shuttlebay, where the team was currently gathered around the TARDIS, while Susan was giving a lecture on its basic principles. It was then, that Grunt tried to headbutt his way in. Grunt's head bounced right off, and he stumbled.

"So, by trying to do that, what have we learned?" She rhetorically asked the Krogan, using a teacher's voice.

"Extrapolator shielding is better at headbutting." He said like a kid in time out, rubbing the plate at the top of his head.

"Why are you all down here?" Shepard asked.

"We came to see the Doctor's box." Garrus answered. "But then she," He pointed to Susan, "started giving a lecture on how it worked. I'm pretty sure most of it was just bullshit technobabble."

"Oh, come on. I'm sure that only ninety-nine of it was." Shepard joked.

"Right, best be off!" The Doctor said, as he and Susan entered. "Don't want to linger too long, otherwise it's gonna get awkward." He stepped in fully, and shut the doors.

"Okay, I'm going to be going on a little trip with the Doctor." Shepard began. "Until I get back, Garrus is in charge." Shepard then followed the Doctor, slamming the door.

"You ready?" The Doctor asked, he and Susan at the controls.

"Sure, why not?"

"Then hold on!" The Doctor shouted. He pulled the dematerialization lever, and the console room shook as the TARDIS took off into the vortex.


	19. Gallifrey

_Gallifrey_

A middle-aged blonde man in ornate armor walked quickly through the halls of the Capitol. He entered a small room, with a table in the center, with holographic projections above it.

"Commander Maxil." The General looking over the holograms saluted.

"Skip the pleasantries." Maxil responded seriously. "As I understand it, there's been a breach in the transduction barrier."

The General activated something on the table, and the hologram switched to a projection of Gallifrey, a blue bubble surrounding the planet. The General focused the hologram on one particular area of the bubble, with a small section of it highlighted in red.

"The breach?" Maxil assumed.

"Yes. Whatever broke through the barrier is of Time Lord origin." The General said. "Otherwise, it wouldn't have made it into the system in the first place."

Maxil stroked his chin, deep in thought. "No one has left Gallifrey since Morbius was in office. So, who could it possibly be?"

* * *

The TARDIS shook and spluttered and the console sparked as it flew through the vortex.

"What the hell's happening!?" Shepard demanded as she and the others were wildly thrown about the console room.

"We've hit the transduction barrier!" The Doctor explained, as he tried to steady the TARDIS. "Think of a really strong bubble -well, it's nothing like that, but if it helps, think of a bubble- surrounding the planet that only lets certain things through, like the TARDIS!" He shouted over the alarms that were blaring. "The problem is, the barrier recognizes the TARDIS as authorized, but the TARDIS doesn't recognize the barrier. She thinks she's in danger, so she's trying to avoid it!"

"What if we shut down her engines?" Susan suggested.

"What good would that do?" The Doctor responded.

"We'd keep our forward momentum, and drift harmlessly through the barrier."

"Don't be silly, that would never... Susan, you're brilliant!" The Doctor shouted, as he started typing something into the keypad on the console at lighting-fast speed. "And..." He flicked a switch and threw a lever, and instantly, the TARDIS calmed. The alarms cut off, the ship stopped shaking, and the console stopped sparking. "There we go! Oh..." He said, as the room started heating up. "We should all probably hold on to something."

"What's happening _now_!?" Shepard shouted, as she tightened her grip on the railing.

"Oh, you know... I disabled the exterior anti-gravity, so now, we're plummeting to the planet below." He sheepishly admitted. The console room violently shook again, rocking everyone inside. "And now, we've hit the upper atmosphere." He pulled a monitor around to face him, and he gripped tightly onto the console. The monitor displayed a diagram of Gallifrey's atmosphere, divided into sections. The TARDIS had hit the uppermost part, but was plummeting at breakneck speeds through it, to the ground below.

The console room started to cool as the uppermost section grayed, and the one below highlighted. "We're in the lower atmosphere! Hold on tight!" The Doctor shouted.

The TARDIS hit the ground, and everyone inside was thrown to the floor from the force of the impact.

"Ugh..." Shepard groaned. "Are both of you alright?"

"Yeah, fine, I'm just..." The Doctor responded, winded. "Susan?"

"Alright." She said, standing up and cracking her neck. "Ow, that's going to hurt later. Where did we land?"

"On Gallifrey." The Doctor unhelpfully responded, as he and Shepard got up. He limped over to the console, and checked one of the gauges on it. "Outer plasmic shell integrity is at seventy-five percent. We should be safe."

"Doc, remind me never to get in a car with you." Shepard said, clutching her sides.

"I'd imagined you'd say that." The Doctor responded, looking at a different scanner on the console. "Hmm... There are definitely Time Lords here. Lots and lots of Time Lords."

"But where are we?" Susan asked. "What city?"

"Well, according to my handy-dandy map system..." The Doctor peered into the oval-shaped screen sat into the console. "We're near the Capitol, on a beach about ten or so miles away." He walked over to the railing, pulled his jacket off, and put it on. He walked over to the door, gingerly pulled it open, and stepped out, as the others followed.

Gallifrey was beautiful. Simply beautiful. Copper colored waves crashed against deep orange sand. Overhead, the sky was a radiant burnt orange, and the two suns lingered overhead, shining brighter than Earth's sun could ever hope to be.

Shepard was pulled out of her observations by the Doctor, who pulled her and Susan along with him as he strolled into a more grassy area.

The grass was a deep scarlet, and the trees in the distance had leaves that seemed to be made of silver. As they walked, the three passed through a meadow containing flowers of every color of the rainbow. In the even further distance, two mountains poked up out of the ground, surrounding a large glass sphere shaped almost like a snowglobe, in which lied an entire city.

"That is the Capitol." The Doctor told Shepard, seeing her staring intently at it.

"It seems... familiar." Shepard said. "This whole place does."

"Good." The Doctor said.

They walked for an hour, taking the time to look at and savor Gallifrey's majestic scenery as they passed it by. Shepard even saw a flutterwing at one point.

Eventually, they came to the outside of the Capitol, and stood in the shadow of the mighty structure.

"How are we going to get in?" Shepard asked. "I don't see any doors."

"There are transmat stations to transport visitors in and out -though we probably don't want to use that, given that we're unauthorized." The Doctor thought about it for a moment, and snapped his fingers as he got an idea. "There are emergency evacuation tunnels that cover the entire interior of the Capitol. If we can crawl into one of those, we can get inside without any sort of pesky security checks. And then one we're in, we can find someone to help with those memories of yours. Let's go."

He led the other two towards the wall of the Capitol, and around it. Eventually, they came to a large sideways rectangular vent, and the Doctor climbed in, pulling up Susan, and then Shepard.

"Don't we have to worry about any security systems?" Shepard questioned.

"Shepard, have I ever told you the story of how I stole the TARDIS?"

"You _stole it!?"_ Susan nearly shouted.

"Yes, but that was a long time ago. The Time Lords are arrogant. They'd never think that anyone would be so bold as to break into their home, so they just don't bother with security in these tunnels. Besides, they're used for evacuations only anyway. Because of that, I could just waltz right in, jump into any TARDIS I chose, and ran."

The three were nearing the end of the tunnel, but the Doctor stopped in his tracks, signaling for the others to stop too.

"What is it?" Shepard asked.

"Shh!" The Doctor said. From outside the tunnel, a deep whirring sound reverberated off the walls. "It can't be..."

"Doctor?"

"Not here, not now!"

"Grandfather, what is it?"

"The most evil creature to have ever existed in all of the cosmos. It's a Dalek."

"Correct." Another Dalek proclaimed, coming up behind the group. "By order of Commander Maxil, you are under arrest!"

"'They don't bother with security' is what you said?" Shepard angrily remarked.

"Yeah, we get it." The Doctor froze, as he realized something. "What'd you just say?" He directed to the Dalek.

"By order of Commander Maxil, you are under arrest!" The Dalek repeated, the lights on the top of its dome lighting up as it did so.

"Well," The Doctor smiled, "This is new."

"You will come with me!" The Dalek ordered, moving forward to force the three out of the corridor.

"So, how do we escape?" Shepard asked the Doctor, whispering in his ear.

"We don't." The Time Lord answered.

"What do you mean? It's just a pepper pot with an egg whisk and plunger for arms! It can't do anything!"

"Shepard, a single Dalek can destroy an entire city." The Doctor outlined. "If we try to run, we'll be dead before we can even get a foot away."

"Then what do we do?"

"For now, we follow their orders."

* * *

"Commander Maxil." A Dalek with black casing addressed, entering the room.

"Dalek Prime." Maxil returned. "I assume you have found the one responsible for the breach?"

"Correct. Three unidentified intruders were apprehended in the lower levels." Prime reported. "Their TARDIS has also been recovered."

"Have they been identified?" Maxil inquired.

"Yes. The youngest and oldest intruders correspond to the missing Theta Sigma."

"That's just what I need." Maxil frowned. "A First Law breaker." Maxil shook his head. "And the third intruder?"

"DNA corresponds to ancient records. Records identify her as 'Arkyitor', granddaughter of the Other."

"The Other?" Maxil repeated in surprise. "So, those damned cultists were right. He did exist." Maxil thought about the issue for a moment. "Have the three of them brought to my office. I have questions for them."

* * *

As the three were being led along by the Dalek, it abruptly stopped.

"I obey!" It suddenly said, as if responding to something. It then turned its dome around to look at the three. "You will remain still."

The Doctor was just about to question why, when he started feeling the air around him electrify. A bright flash of blue light interrupted his thoughts, and the three were transported across the Capitol.

"Greetings." The Dalek behind the teleport terminal said to the three. "I am Dalek Prime. You will follow me."

The Dalek wheeled out of the room, and the three followed it. Prime led them through the sprawling halls of the Capitol, to a door at the end of a long hallway.

"You will enter." Prime ordered.

The doors swished open, and they stepped into the room.

The room was very spartan, with only a simple desk, chair, and terminal being the only things that sat inside the room.

"For eight-hundred years, _no one_ has left Gallifrey. Not even to go to orbit." The man in the chair began, looking out the window. "So imagine my surprise, when not only do I hear that a TARDIS has broken through the barrier and it has successfully landed, but the culprits are the infamous Theta Sigma." He turned the chair around, revealing his face.

"Commander Maxil." The Doctor recognized.

"Infamous?" Shepard questioned.

"The abduction of Theta Sigma is one of Gallifrey's very few unsolved crimes." Maxil started. "At the very end of President Morbius's term in office, just before the Great Retreat, the oldest Time Lord of Lungbarrow house, one Irving Braxiatel, just up and vanished, along with the youngest of the house, without any warning whatsoever. The motive? Undetermined, even to this day. Not even the Matrix knows why he did it. Now, that very missing child has returned, and we can get answers, and Braxiatel can finally be put to justice. So," Maxil leaned on his desk, locking his hands together, "Why did he do it?"

"Uh..." The Doctor rubbed his head. "Not too sure about that one. Still working it out myself, actually. But Brax never did _anything_ without some kind of motive. I can, tell you though, that because of his actions, Commander Shepard here has stopped the galaxy from being harvested by giant genocidal machines."

"Commander Shepard?" Maxil repeated in distaste. "That follows the human naming conventions... Don't tell me the two of you _lived_ with those backwater yokels!"

"Backwater yokels!?" Shepard's eyebrows skyrocketed.

"Yeah, uh... A lot of species as a whole sort of see humanity as the hillbillies of space." The Doctor admitted reluctantly. "Sorry."

"You've gotta be fuckin' kidding me." Shepard said, bemused.

"Enough!" Maxil barked. "It's time we got back on topic. You say you don't know why Braxiatel committed the crime?"

"No." They shook their heads.

"Then I suppose I'd better focus my attention on the more pressing issue. The blatant violation of the First Law that you've all committed."

"Oh... That." The Doctor said. "About that, you see... She's not me."

Maxil's eyebrow arched.

"I'm from a parallel universe." The Doctor explained. "If you examine my biodata, then you'll see it for yourself."

Maxil continued to hold his eyebrow in that position, even as he pulled a very complex scanning device out of his desk. He ran the device over the Doctor, then Shepard, the device beeping loudly as it did so.

"Well, it seems you're telling the truth." Maxil frowned. "However, you have still broken through the transduction barrier. A capital offense, for which the only sentence is permanent execution."

"You can't!" The Doctor shouted.

"Please, there must be something we can do!" Susan pleaded.

"...Perhaps." Maxil said after a moment. "Several TARDISes were recently stolen from their cradles at the shipyards. If you three can find the culprits, and bring them to us, all charges against you will be dropped."

"We'll do it." Shepard said for the others.

"Excellent." Maxil said. "A tetherlock has also been placed on your TARDIS. It will be released once you've completed your task. Go." Maxil turned around, and started gazing back out the window, while the three left.

* * *

"I can't believe they put a tetherlock on you." The Doctor grumbled, stroking the TARDIS's console. "You did nothing wrong."

"Are you _petting_ your spaceship?" Shepard asked, incredulous at the sight in front of her. "And I thought Joker was bad."

"The TARDIS just isn't a ship, Commander." Susan explained. "She's a living organism. Granted, she isn't alive in the same sense as you and I, but she's alive nonetheless."

Shepard sighed. "So, just how are we going to find the stolen TARDISes? They could be anywhere!"

"Not quite." The Doctor said. "TARDISes can't travel through the vortex without a Rassilon Imprimatur. Without it, they'd disintegrate the moment they entered. And TARDISes will only bond with Time Lords that they _want_ to bond with. It's likely that a number of them didn't take too kindly to being stolen, and refused to bond. Meaning they'll still be on Gallifrey."

"So then how do we find them?"

"Hmm..." The Doctor stroked his chin, then he snapped his fingers. "Just before the Time War broke out, they invented a way to track TARDISes based on the distortions they created in space. If we can find distortions that fit the bill of a concentrated group of TARDISes, then we find where their hijackers are hiding out." He explained, activating the TARDIS's scanners. He stared intently at it for a moment, before yelling out: "Got them!" He pulled the lever, and the TARDIS set into motion.

* * *

The TARDIS's blue Police Box form faded into view in a large expanse of crimson sand. The doors swung open, and the three time travelers stepped out.

"Great, a desert. I can see all of the TARDISes from here." Shepard deadpanned.

"Shh!" The Doctor said, holding up his hand. "I can hear them."

"The TARDISes?" Susan assumed.

"I can't hear anything." Shepard shook her head.

"Because you're not accustomed to using your telepathy." The Doctor explained. "Here, let me." The Doctor approached Shepard, and pressed both of his hands to her temples.

Instantly, Shepard could hear the sound of crying infants. But she couldn't just hear them, she could _feel_ them. Their pain, their fear... every last ounce of it was poured into Shepard's head. "Those are the TARDISes?" Shepard asked, starting to shake very minutely.

"Yes." The Doctor confirmed. "Maxil said they were stolen from the shipyards. They're just babies at this point. And they're scared out of their wits, taken against their will..." The Doctor fumed.

"...Get rid of it." Shepard begged, on the verge of breaking into tears completely.

The Doctor removed his hands, and the sounds and feelings Shepard was experiencing faded.

"How could someone do something like that?" Shepard wondered.

"Sadly, most Time Lords don't see TARDISes as anything other than an advanced form of transport." The Doctor shook his head. "But they're so much more. They co-evolved with us. Beautiful creatures, with a greater understanding of the fundamental workings of time than even the oldest or wisest Time Lord. And we practically enslaved them." He spat in disgust. "It's disgraceful." All of a sudden, his eyes widened as he realized something.

"What is it?" Susan asked as she saw the Doctor trying to work something out.

"Why would someone try to steal a baby TARDIS? It doesn't make sense." He frowned. "The control mechanisms aren't installed until they reach the second stage of their life cycle, and they aren't even ready to bond until the _third_ stage... Oh well, I'm sure I'll figure it out." He clapped his hands together, suddenly switching moods. "We've got thieves to catch. But there's only one problem: We're in a desert!" He suddenly shouted to the heavens, startling the other two, especially Shepard, who had been standing right next to him. "Sorry," He apologized. "Heastroke. Honestly, who puts their secret hideout in the middle of a desert?"

"People who don't want to be caught, maybe!?" Shepard shot back, rubbing her ear. "I'm getting you back for that, by the way."

"Yeah, whatever." The Doctor disregarded, literally hopping up and down. "Does this sand seem stiff to you?"

"Stiff?" Susan questioned, rubbing her hand on the sand close to the Doctor. The stand still moved, but it took a lot more effort on Susan's part. "The sand shouldn't be like this."

"That's because it isn't sand." Shepard assumed.

"Good eye." The Doctor complimented. He crouched down, and promply licked the sand. "Huegh!" He spat the sand out. "Not sand- nanobots. And they're hiding something." He stepped off the patch of sand, and whipped out the sonic. Extending it, he pointed it at the sand. He pressed the activator down, and the sand shifted aside, revealing a staircase leading down. "Ah ha! A secret passageway!" He grasped the screwdriver, pushed the extended part back down, and returned it to his pocket."You'd think that someone who didn't want to be caught would take a bit more precautions. But never mind that-let's go!" He said, strolling down the staircase.

Susan and Shepard followed him, and the fake sand returned to its normal position as they proceeded.

"So, a group of people who've done nothing but stolen TARDISes, with a secret hideout in the middle of the desert... Who do you think it could be?" The Doctor wondered.

"They could be the Faction." Shepard shrugged, the Other taking hold for a moment. "Rassilon, Omega, and I had a few run-ins with them. They tried to seize our early time travel protoypes and destroy them, causing a paradox. And there's no greater paradox I can think of than merging the same TARDIS just in different points in its own timestream." She theorized. "Shit, I did it again, didn't I?" Shepard asked, suddenly lucid again.

"Yeah, you did." The Doctor said. "But that's not a bad theory. But that just begs another question: Why would they want to steal the babies?"

"Maybe they're making paradoxes by removing a TARDIS from a point that it's already established as being at?" Susan guessed. "It's not exactly the biggest paradox, but it's still a paradox nonetheless."

The three continued down the hall, coming to an intersection. They debated on which direction to proceed, but couldn't come to a decision. A weapon charging was heard, and a bright flash illuminated the room, and the three fell to the floor, unconscious.

* * *

The Doctor jolted awake, and took in a deep breath as he regained consciousness. He looked around, and examined his surroundings.

He was in a large chamber, about as big as the cloister room in the TARDIS. He, Shepard, and Susan were tied up in the center of the room, in front of a large throne, and large coral-looking cubes were lined up against the walls.

The lights activated, and several people walked it, surrounding the three on all sides.

"Why do I get the feeling we're in trouble?" Shepard deadpanned, as she woke up.

"Trouble?" A female voice reverberated off the chamber's walls. "Now, what gives you that impression?" The woman asked, strolling into the room, and sitting on the throne.

"It can't be..." The Doctor breathed, looking at the woman. He hadn't seen her in a long time, and she had changed quite a bit, but he could recognize her.

"Oh, so you actually remembered something. That's a first." The woman said, leaning back. "For a second there, I thought I was going to have to fill you in. Again."

"Grandfather, who's she?" Susan inquired.

"She's... It's complicated."

"Oh no, she isn't an ex-girlfriend, is she?" Shepard dryly remarked.

The woman's eyebrows raised. "I like this one." She said, pointing at Shepard. "You should definitely keep her." She uncrossed her legs, got up, and approached the Doctor. "How's the old Type 40 doing?"

The Doctor shrugged, at least, he tried. "Pretty good, all things considered. Especially after the business with the Edifice and all that... How are you?" He awkwardly returned.

"A little obsolete. Especially after they introduced the 105s."

"Sorry... I'm not following." Shepard spoke up. "Who _is_ she?"

"You know how I said the TARDIS was a sentient life-form? Well, some TARDISes are a bit more... human than others." The Doctor explained. "Shepard, Susan, meet the first (and only) Type 102 TARDIS, Compassion."

"...eh?" Was all that could be formed by Susan.

The Doctor rolled his eyes. "Keep up, Compassion here's a TARDIS. The most advanced one to have ever existed. By the way, don't let the name fool you. She's anything but."

"Oh, you wound me." Compassion placed a hand over where her heart would be. "Is that any way to treat someone who literally carried you around for years?"

"When that someone's internal architecture turned homicidal based on her menstrual cycle equivalent? Yes, it is. Now could you let us out? I can feel the rope digging into my wrists."

"When just a second ago you all but insulted me?" Compassion returned, crossing her arms. "Nah, I think I'll leave you here. Besides, Shepard looks quite nice where she is..."

"That's Susan." The Doctor corrected.

"And that was wrong on so many levels." The actual Shepard shuddered.

Compassion sighed. "You'd better not make me regret this. Do you remember the last time we got in trouble with a rope?"

The Doctor flinched as Compassion undid his bindings. "You think Fitz has forgiven me for that yet?

"I don't know, those were some pretty intense rope burns." She said, as she moved on to undoing the others' bindings. "I can still feel them, you know."

"I said I was sorry! And besides, the cow didn't get hurt." The Doctor tried to justify.

"The cow didn't actually climb the rope, it was being carried by me!"

"Oh, are you guys talking about the adventure involving the pickle?" Susan asked excitedly. "The one that almost started intergalactic war?"

"How does a pickle start intergalactic war?" Shepard asked.

"Through a very careful combination of espionage, sabotage, the kidnapping of a sacred heifer, and a political assassination or two." Compassion said, as she finished with the rope.

"Sure, cause that explains everything." Shepard deadpanned, as she got up. "But shouldn't we get on to why we're here?"

"Good plan." The Doctor pointed at her.

"Can't you talk for one second without gesticulating like a madman?" Compassion asked.

"Probably not, now," He got serious. "Why have you kidnapped a bunch of baby TARDISes?"

"Kidnapped!?" Compassion raised her voice. "I'm not kidnapping them, you git! I'm trying to set them free!"

"Oh... I suppose that makes a sort of sense." The Doctor sheepishly admitted. "It's just the lot of them crying gives off the wrong impression."

"I know! I've tried everything to get them to stop, but nothing works."

"Have you tried singing them a lullaby?" Shepard sarcastically asked.

"TARDIS lullabies are a lot more complicated than human ones." The Doctor said.

"Really? There's such a thing as singing a living timeship a lullaby?"

"No. But I had you going for a moment, didn't I? So," The Doctor clapped his hands together, "if the baby TARDISes aren't being used for nefarious purposes, then I suppose it can't hurt to let you set them free. But what do we do about Maxil? If we don't report back to him, or tell him something he doesn't want to hear, then he executes us." He rubbed his chin in thought for a moment, then he snapped his fingers. "I've got it! Compassion, you get the tetherlock off the TARDIS, and I'll transport you and the baby TARDISes to a planet of your own. Deal?"

She thought about it for a moment. "...Deal."


	20. Remembrances

**_I'm so sorry it took a bit longer than usual to get this one out, but you know what they say: Real life's a bitch._**

* * *

 _The Doctor's TARDIS | High Gallifrey orbit._

"Hyperspanner." Compassion requested, holding out her hand. She was currently under the TARDIS's console unit, trying to break the tetherlock.

The Doctor handed the humanoid TARDIS the requested tool, and stood around, looking bored. "So, how'd you get here?" He inquired. "Not in here, but in this universe."

Compassion shrugged. "The Time War broke out, the walls of the universe started sealing, and I decided I didn't want to be caught in the crossfire, so I jumped ship before they snapped shut all the way. How did _you_ get here?"

"It's a long story." The Doctor sighed. "I used to travel with people before I picked up this universe's Susan. Amy and Rory Pond." He reminisced fondly.

"A married couple? That seems so unlike you. If I remember right it wasn't the torture and traumatic events that drove you insane, it was settling down."

"Well, the Ponds were a pretty special case..." He smiled to himself. He lost his smile as he began to remember their last adventure. "We were in New York, when Rory got sent back to the 30s by a Weeping Angel. We tried to go in save him, and made a paradox that would poison the angels' food supply, but... He still got sent back. And then Amy let herself get touched by the angel." Tears gradually filled the Doctor's eyes. "They always leave, don't they? Everyone I travel with goes at some point. Even Susan's bound to leave one day..." He straightened his bow tie, and blinked away the tears. "Anyway, the TARDIS decided to bring me over here for some reason. Still trying to work that out. But enough of that, how's it going so far?"

"It's going damn tough." Compassion gritted her teeth. "They locked this thing tighter than a virgin in a chastity belt."

The Doctor sighed. "Let's hope Shepard and Susan are having a better time than us."

* * *

"I don't like it." Shepard said, looking at one of the baby TARDISes.

"Why not?" Susan asked, as she tried to coax one of the TARDISes activate its chameleon circuit to change into something that she could carry.

"It's like it's staring at me." Shepard commented. "Accusing me."

"Accusing you of what?"

"I don't know, it just feels like it's peering into my soul."

"It's probably trying to gauge whether or not you're a suitable pilot."

Shepard flinched. "I'm terrible at piloting. Have I told you what happened to the mako the first time I tried to drive it?"

Then, the TARDIS that Shepard was in front of started to suddenly glow white-hot, and morphed into the Mako's hybrid truck-tank shape.

The Commander blinked. "That was easy, but I don't think a Mako can fit through Police Box doors." Shepard shook her head. "How do I get it to go smaller?"

Susan shrugged, as she still attempted to get the TARDIS she was working with to change. "I don't know, just ask it, I suppose."

"Umm, TARDIS..." The Commander addressed awkwardly. "Could you maybe get a little smaller, change into like a little toy or something?"

The Mako started to glow, and it shrunk down, getting taller and more boxy as it progressed. When the light faded, it revealed a drastically scaled-down version of the Doctor's TARDIS.

"Okay, that's just too cute..." Shepard chuckled as she picked it up. "Can I take you home with me, please? I know a really great model ship shelf that you'll fit on just perfectly."

The tiny TARDIS's lights glowed happily as the Commander talked to it. Or her.

"TARDISes usually don't act like that." Susan commented. "It must like you."

"Yes, I suppose it does." Shepard said, looking at the tiny box she held in her hands. She then frowned as she thought of a question. "If these are supposed to be babies, then how come they have cloaking devices?"

"The Chameleon Circuit is something the TARDISes naturally evolved when they were still a species of coral." Susan explained, as she TARDIS she was talking to finally shrunk down to a basketball. "Predators on Gallifrey were very vicious, and they were comparatively weak, so they developed the ability to hide from predators by taking the form of inconspicuous objects, like rocks and trees." She then bent down to pick up the other TARDIS. "Or a basketball."

"Or ancient video game consoles." Shepard said, suddenly on the other side of the room, looking down at a NES. She shook her head, and picked it up. "So, how much's that so far?"

"Three. Out of twenty."

Shepard sighed. "Then I suppose we'd better get to work."

* * *

 _A few hours later_

"Finally." Shepard sighed, flopping down on one of the chairs in the console room. The console room was filled with various knick-knacks and junk, actually the TARDISes. "Can we leave now?"

The Doctor looked up from the console controls in confusion. "I thought you wanted help sorting out your memories?"

"That was before we'd all be executed trying to do it."

"I might be able to help with that." Compassion said, extending an offer. "Not with the executing part, of course, but I can help with your memory."

Shepard got up, and approached Compassion. "Okay... So how's this going to work."

"If I'm not mistaken, the Doctor briefly changed into a human for... whatever reason, locking his memories away. But he couldn't get rid of his ones as the Other, so his TARDIS held them back. This is going to work a little in reverse, I'm going to bring your memories as the Other to the forefront, and allow them to safely merge with the memories you have now. By the way, try not to move at all during this... It won't end well." Compassion's eyes flashed gold, and Shepard collapsed to the ground.

"...Crap."

* * *

"Hello!?" Shepard shouted out. "Doctor? Susan? Compassion! This is such horseshit, is anybody even out there!? I know you can hear me, goddammit!"

One moment, she was standing in the TARDIS control room, and the next, she was surrounded by absolute darkness, extending in all directions.

Then, the entire area became bathed in blinding white light, as a baby started crying.

 _"There's the head!"_ She heard someone shout.

The light kept becoming more intense, forcing Shepard to cover her eyes.

 _"...The arms!"_ She heard the same voice shout.

The light became so intense, that not even covering her eyes could keep it out.

 _"He's out, you can stop!"_

The baby continued to cry as the light died down, revealing something resembling a hospital room, filled with human-looking people.

Then, all of a sudden, the scene changed. Shepard was now in a large field, red grass extending in all directions.

 _"Run!" A little boy yelled, as he and another were running from three others._

 _"What do you think I'm doing!?" The boy in the red Time Lord robes shouted back._

 _But then, the two of them tripped, and the three giving chase caught up, and started beating on them. It lasted for all of about five minutes, before they left._

 _"...I hate you." The boy in the robes directed to the other._

 _The other boy chuckled. "I hate you too, Rassilon. Oh, that's going to hurt in the morning."_

Abruptly, the scene changed again. Shepard was now in a sort of lecture hall, filled with what looked to be college-aged students.

 _"I'm telling you, Rassy, if we do this, we become legends!" The Other excitedly whispered to his friend._

 _"No, we become compressed down to the size of a peanut._ " _Rassilon retorted._ _"Messing with a stellar manipulator is like playing with a loaded staser, it can only end in misery."_

 _"So we ask Omega to borrow his." The Other sighed as he saw the look on Rassilon's face. "You didn't fight in the Vampire Wars just to be stuck on one planet afterwards, did you? Look, the theory's sound, and we've got all we need already! What's the harm?"_

 _"...Fine. But if my family has to bury an atom, I'm haunting you."_

Shepard's surroundings changed again, this time she was in a ship, with an older Other and Rassilon, and alongside a third figure.

 _The Other whistled. "Now THAT is a star!"_

 _"It will make the perfect candidate for the Eye of Harmony." Omega agreed._

 _"I dare say, this has been quite the adventure!" The Other smiled._

 _"What 'adventure'? We've just been wandering around for half a century, strictly business." Rassilon grumbled._

 _"I don't think the woman back on Eve would agree." The Other wiggled his eyebrows._

 _"Enough, you two." Omega said. "Let's get this done, shall we?"_

 _The Other nodded, suddenly completely serious. He walked over to a terminal, and started feeding it commands. Then, the star outside started to shrink._

 _Then, the ship started to shake violently._

 _"It's shrinking too fast!" The Other reported. "We're caught in its gravity well!"_

 _"I can't shut down the hand from here." Omega calmly stated, standing up. "I must go do it manually. You two keep the ship from falling into the star."_

 _Omega left the room, and but a moment later, a large chunk of the ship broke off, as the star began to slow._

 _"You did it, Omega." The Other spoke into the intercom. "...Omega?"_

 _The only thing that came back, was static._

Once again, her surroundings changed, this time to a very extravagant office.

 _"You son of a bitch!" The Other shouted, storming in. He slammed his hands down on the desk where Rassilon was sitting. "You've gone too far!"_

 _"My dear fellow, I have no idea what you're raving about. Perhaps if you explained it calmly?" Rassilon condescended._

 _"You know damn well what I mean! Maybe you thought I wouldn't figure it out, I was always 'the fool' of our group, but I did. I know for a fact that Omega's demise wasn't an accident."_

 _"It would do you well to watch your tongue in here." Rassilon said, deathly serious._

 _"The others may not know, but they will." The Other vowed. "I'll make sure that they never forget what you've done!" Then, he stormed out of Rassilon's chambers, leaving the president on his own._

The scene changed again, this time to a very ornate room, with a large cylindrical object in the center of it.

 _"Grandfather, please!" Arkyitor begged. "Don't do this!"_

 _"I must, my dear." The Other responded, now an elderly man. "As long as I remain alive, Rassilon will keep threatening you and the family, and I simply cannot have that."_

 _"But there has to be another way!"_

 _"Alas, there is not." The Other shook his head, and Arkyitor started to cry. "Don't weep, my child. One day, I shall come back. Yes, I shall come back. Until then, there must be no regrets, no tears, and no anxieties. Just move forward in all your beliefs, and prove to me that I am not mistaken in mine. Now, we must proceed." The Other hurriedly went over to the tube, and opened a door, stepping inside. "Goodbye, Arkyitor."_

 _The young Gallifreyan just nodded, and pressed a button on a control panel a few meters away from the tube. The inside of the tube lit up bright with a golden-orange glow, bathing the room in light. A moment later, the glow diminished, and the Other was gone._


	21. The Justicar

**_I'm really sorry this one took so long to get out. I got hit with an extreme case of writer's block again. And since I've always had a policy of 'Update when it's ready' that really can't be helped._**

* * *

"Shepard, wake up."

The Commander opened her eyes to see the Doctor's face over her. Shepard groaned, shook her head, and got up off the TARDIS's floor. "What happened?" She inquired.

"You collapsed like a bunch of bricks." The Doctor said. "I can only assume it's because of Compassion sorting through your memories. How are they?"

"Honestly, I only really got the general details." Shepard answered.

"Oh... Well, I suppose that's for the best." The Doctor stated. "We can't have you running around with all sorts of forbidden knowledge, can we?"

"I guess not." Shepard agreed.

"I've went ahead and dropped Compassion off on an unsettled planet. She'll be free to do whatever she plans with the baby TARDISes in relative peace. We can head back to the Normandy whenever you're ready."

"Then what are you waiting for?" Shepard rhetorically asked. "Get us back."

The Doctor nodded, and set the TARDIS into motion. Moments later, the engines ground to a halt, and the timeship settled. Shepard moved to open the door and looked out, before realizing-

"This isn't the Normandy." Shepard noted, looking out at the massive Asari city in front of her. "Does this happen on a regular basis?"

"Not... really?" The Doctor lied, moving towards the scanner. "According to the map, we're on Ilium, an Asari colony. Don't worry, I'll have us back on board the Normandy in to time."

"Wait." Shepard interrupted the Doctor's movements. "The next two people I'm supposed to recruit are here on Ilium."

"Well, I suppose that saves us a bit of time." The Doctor conceded. "So, if you're wanting to recruit them, who do you want to go for first?"

"We should go for Samara first." Shepard replied. "I get the feeling that we won't be needing an assassin for the moment."

"Right." The Doctor nodded, throwing on his coat. "You should... suit up? I think that's the term. I hope it is. I don't keep guns aboard, you understand, but there should be some suits of armor hidden in the back of one of the storerooms."

Shepard nodded, and went off to go find what she was looking for. Moments later, she came back, wearing a hardsuit very similar in appearance to the armor that stereotypical knights wore.

"Why do you have one of these?" Shepard wondered, looking at the gauntlets on the armor.

"I borrowed it." Was all he said. "Susan!" He shouted into one of the corridors. "Shepard and I are going out, you're in charge of the TARDIS while we're gone. No joyrides!"

"Got it, grandfather!" Susan shouted back. "You two have fun on your date!"

The Doctor did a double-take. "Th-that is just wrong on so many levels!" He then sighed, and turned to Shepard. "Well then, let's be off." The Doctor said, opening the door, and stepping out. "Any idea where we are?" He inquired, looking at the unfamiliar surroundings.

"No idea." Shepard truthfully replied. "I don't make it a habit to travel to planets that legally condone slavery. Or as they would call it 'indentured servitude.'"

"'A rose by any other name smells the same.'" The Doctor agreed, using as quote that shouldn't have fit the situation.

"Did you just quote who I thought you did?" Shepard questioned.

"I quote lots of people." The Doctor retorted, as he and Shepard walked along.

"But Shakespeare?"

"Who d'you think came up with that one in the first place?" The Doctor responded, with a slight twinkle in his eye.

"No... You're shitting me!"

"I most certainly am not! Poor old chap came down with a case of the flu, so I had to finish some of his stuff for him while he got better."

Shepard just scoffed in disbelief as a response. "Any other famous authors you filled in for?"

"Well, I gave Jules the inspiration for writing Journey to the Centre of the Earth. Then there was that business with Agatha Christie that bled into some of her works, but then again, that wasn't really _filling in_ per say... After that I met Douglas Adams. Splendid fella, that one. Gave him the inspiration for Dirk Gently. Then I had to write out about a quarter of the Declaration of Independence. And don't even get me started on the Treaty of Versailles."

"You're not serious."

"As serious as spoiled custard and rotten fish-fingers... Okay, I wouldn't go that far." After shaking his head at his last statement, something caught the Time Lord's eyes. "A police station... Perhaps they have some idea where we can find Samara?"

"Good eye." Shepard complimented, leading the way into the police station, as the Doctor followed with a look of pride on his face.

The two passed through the entrance, and walked up to the Asari detective at her desk.

"Commander Shepard." The Asari addressed, recognizing Shepard. "Welcome to my district, I'm detective Anaya. What can I do for you?"

"We're looking for a Justicar named Samara." Shepard truthfully answered.

"If you've got a score to settle with Samara, take it somewhere else." The detective sternly replied. "I've got more than enough trouble already."

"All I need to do I ask for her help with something, and then we'll be on our way." She outlined, gesturing to herself and the Doctor.

"Justicars usually work alone, but they they tend to be drawn to impossible causes." Detective Anaya stated.

"Well, I suppose that's step one complete." The Doctor piped up.

"If you want to get her out of my district, I'll get you to her ASAP." Anaya offered. "She's at the crime scene. It's outside and on the right of the station."

"You seem awfully anxious to get her out of here." Shepard noted.

"My bosses want me to detain her. They're afraid she'll cause a cross-species incident. But that code of hers won't let her be taken into custody. If I try it, she'll have to kill me." She explained. "I have no interest in dying, so if you lure her away with some big noble cause before I have to carry out my orders, I'll be glad to help you."

"Then I suppose we'd better get this done before you have to take her in." Shepard said, moving to the door.

"Hold on." The detective said, stopping Shepard in her tracks. "That crime scene's Eclipse territory. They'll slaughter you if you don't have a gun." She approached the weapons locker sitting in the corner of the station, and pulled an Eviscerator shotgun out of it. She approached Shepard, and handed it to the Commander. "It's the only one I can spare, so don't lose it. Good luck."

Shepard nodded, and she and the Doctor left the station, heading around the corner, through the police line, and into the alley. There were three mercs clustered together, talking amongst each other.

Shepard activated her omni-tool, and fired an incineration blast down the alley, setting one of the mercs alight. The other two frantically scrambled to take Shepard out, only to be stopped by their guns not firing.

"Now," The Doctor began, lowering his sonic screwdriver, "you two can try to fight my associate here, and be killed. Or you can run, and live to see another day. What do you say, eh? No hard feelings?"

The two mercs looked at each other, nodded, and readied their omni-blades, charging at Shepard.

But that proved to be especially stupid, because as soon as they got within range, Shepard unleashed the full power of the shotgun at them, shredding into them, and leaving them dead on the floor.

The Doctor shook his head, simply saying nothing as he gingerly stepped over the bodies, and followed Shepard through the door at the end of the alley.

As the two went through, an Asari Eclipse member slammed into the wall next to them, falling to the floor in a heap.

Further in the room, Samara herself was facing off against another Asari as she glowed with blue Biotic energy.

"Those were my best troops!" The Eclipse merc said, shaking with fear.

"Tell me what I need to know, and I will be long gone from here. Where did you send her?" Samara demanded, her voice cold and unfeeling.

"You think I'd betray her?" The other Asari asked, holding an incredulous tone. "She'd hurt me in ways you couldn't imagine!"

"The name of the ship." Samara repeated. "Your life hangs on the answer, Lieutenant."

"You can kill me, but one of us _will_ take you down, Justicar." The other Asari vowed. She leveled her weapon, and moved to shoot, but was instantly stopped by being lifted into the air by Samara's biotics, and she was thrown through a pane of glass, to the level below.

Samara jumped down after her, slowing her descent as she did so, and the Justicar approached the Lieutenant. The other Asari scrambled to get away, but Samara was faster.

The Justicar put her foot on the merc's neck. "What was the name of the ship she left on?" Samara asked for the final time.

"Go to hell." The other Asari grunted.

Samara stayed silent for a moment. "Find peace in the embrace of the goddess." She said, before twisting her foot, and with it, the merc's neck.

Looking up from the now-dead Eclipse Lieutenant, Samara spotted the Doctor and Shepard approaching her. "My name is Samara, a servant of the Justicar Code. My quarrel is with these Eclipse sisters, but you are well-armed." She directed to Shepard. "Are we friend? Or foe?"

"Friend." The Doctor hastily nodded. "Definitely friend."

"That merc was wounded and helpless. Do you just kill anyone who won't help you?" Shepard accused.

"If my cause is important enough, yes." Samara calmly responded. "Are you different?"

"I've killed people," Shepard shamelessly admitted, "but always with good reason."

"I answer to a code that is clearly define. If my actions are true to that code, I am just. If they are not, I am unjust." Samara explained. "I don't pretend it is a simple matter, or that it seems right to everyone, but I sleep well at night, and that is more than most can say. How may I be of service to you?"

"I'm going up against suicidal odds, and I need the best-that's you." Shepard truthfully answered.

"I sense the truth in what you say, and it humbles me. But I seek an incredibly a dangerous fugitive. I cornered her here, but the Eclipse smuggled her off-world. I must find the name of the ship she left on before the trail goes cold." Samara explained.

"I wish you were willing to go with Shepard, Justicar." Detective Anaya said from nowhere, approaching the group. "I've been ordered to take you into custody if you won't leave."

"You risk a great deal by following your orders, Detective. Fortunately, I will not have to resist. My code obligates me to cooperate with you for one day. After that, I must return to my investigation."

The detective shook her head. "I won't be able to release you that soon."

"You will not be able to stop me." That didn't sound like Samara was making a threat. It sounded like a promise.

"Um, excuse me, if I may." The Doctor interjected, waving his hands about awkwardly. "It sounds like you want her to leave, detective, but her code won't let her until she gets what she wants. But she can't get what she wants if she's in your custody. And you can't release her to get what she wants because that's be disobeying your superiors, right?"

"That's right. What are you suggesting?"

"Well, if Shepard and I were to go get what Samara wants, and bring it back, she'd have no reason to stay, and you'd have no reason to keep her, and we can go our separate ways without one of us dying."

"That is reasonable." Samara nodded. "You should begin by speaking to Pitne For, a Volus merchant. He used to associate with the Eclipse, but now they are planning to kill him. If you speak to him, get the truth out of him, he may know a way into the Eclipse base."

"Well, I've got to get back to the station. And I guess I've got to take you with me." Detective Anaya said with a distinct tone of discomfort as she approached Samara.

Samara nodded, and followed the Detective out of the room.

The Doctor and Shepard followed them out, but headed back to the large area in front of the police station, where a Volus, presumably Pitne For, was standing around, looking perturbed.

"Hello, Earth-clan." The merchant greeted. "What can I do for you?"

"The Eclipse are after you." Shepard began. "I want to know why."

"I know nothing of any mercenaries, Earth-clan." For denied. "I am merely an innocent merchant, trying to make his way in life."

"The Eclipse are out for your blood; I need help to break into their base." Shepard said, getting closer. "Shouldn't we work together?"

Pitne sighed. "Yes. I suppose you are correct, Earth-clan. Let's talk. I smuggled a chemical onto Ilium that boosts biotic power in combat."

"I don't see why they would kill you over that." Shepard interrupted.

"They would not... but the chemical is extremely toxic. I may have -erm- forgotten to mention that to the Eclipse, so now they are furious, and want my blood."

"Well, tell you what: Ill cut you a deal. You get me into the Eclipse base, and I'll get them to stop going after you." Shepard very calmly outlined.

"Into their base!?" The Volus was not as calm. "Why would you want to go in there!?"

"Does that really matter? You want to get the Eclipse off of you, and all I want is to get into their base. Trust me, this is the best deal you can get given the situation."

"...Very well." The Volus conceded. "I did have a passcard to get inside. Well, they took that when they found me out. But I did happen to make a copy. Take it. But be careful, every Eclipse sister commits murder to earn her uniform-no exceptions."

"Thanks for the tip." Shepard said, taking the keycard, before leaving and pulling along the Doctor. The two walked to the back of the police station, and into the waiting elevator. The door slid open, and the two stepped in. "I hope this all goes alright." Shepard suddenly said, as the elevator moved up the shaft. "I don't usually do the whole 'one-man army' thing."

"We'll be fine." The Doctor responded, as the elevator slowed to a halt.

The door opened, and Shepard instantly spotted a mech waiting for them. She reacted immediately and fired at its head, talking it clean off, and causing the mech to shut down. She crouched down, pulled the pistol from its broken chassis, and got one one side of the door. The Doctor got on the other side, and the door slid open, allowing access into a large room, filled with more Eclipse and canisters of the toxic compound that was smuggled in.

Shepard peeked around the corner and fired three shots at the head of the closest Eclipse merc. The first two ripped through her shields, the last one ripped through her head, scattering blood everywhere, and causing the merc to die instantly.

The Doctor, meanwhile, was aiming the sonic screwdriver at the toxic canisters, and pressing the activator down, causing the canisters to explode and scatter their contents all over the Eclipse. While this may have caused their biotic powers to increase in strength, the Eclipse started breathing the chemicals in, and started choking to death. The Doctor grimaced as they all started falling to the floor, dead.

"Now how are we going to get through?" Shepard asked. "That's the only way, and we'll choke trying to go through."

The Doctor turned to Shepard, fixing her with a look of amusement, like he knew something she didn't. "Respiratory bypass. Comes in handy in situations like these. Just take a really deep breath, and hold it." He instructed, doing so himself.

Shepard followed the Doctor's example, and the two ran through the cloud of chemicals, into a safe area. The Doctor pressed the door control, and it sealed behind them, allowing them to breathe. "Ah, the perks of being a Time Lord." The Doctor smiled to himself. Then, he stopped as he heard something. "You hear that?"

"Sounds like someone wallowing around in fear." Shepard answered, heading towards the source. They opened another door, this time with an Eclipse merc hiding behind it, cowering behind a desk. "Get up." Shepard ordered.

"Wait, stop! I didn't fire my gun once! I pretended to because the others were watching, but I didn't really shoot!" The Asari scrambled to say.

Shepard began to lower her gun, but the Doctor piped up.

"Shepard, remember what Pitne said?" The Doctor reminded. "If she's wearing that uniform, then that mean she's already killed."

Shepard nodded, and raised her weapon again, but the Doctor interjected again. "Wait, don't just kill her!"

"Well then, what do I do?"

The Doctor thought about it for a moment, before approaching the Eclipse merc. "Sorry about this." He said, before headbutting her. "OW!" He yelled, cradling his forehead.

"What the hell did you do that for!?" Shepard asked in surprise.

"Needed to knock her out." The Doctor groaned in pain, looking down at the merc. He shook off the pain, and pressed his fingers to her temples. A moment later, he pulled his finger away, and stood back up.

"What did you just do?"

"I put a suggestion in her mind." The Doctor answered. "When she wakes back up, she'll be compelled to go turn herself in to the authorities."

"Can you teach me how to do that?"

"Maybe." The Doctor answered, as he and Shepard exited the room, and proceeded up the stairs. They headed out into another open area, again filled with Eclipse.

Once more, Shepard used her gun to take out the Eclipse, while the Doctor used the sonic to run interference, and the duo proceeded through the base.

They eventually came to a large open area, with the path deeper into the base on the other side of a bridge.

"It seems kind of... empty here, doesn't it?" The Doctor commented as he and Shepard walked across the bridge.

As if in direct response to his comment, a gunship flew up directly in front of them.

"Doctor, into cover!" Shepard shouted, as she dove into cover. The Doctor followed, and now both of them were trapped as the gunship fired on their position.

"Any ideas?" The Time Lord shouted.

"It's not like I can take it out with a pistol!"

The Doctor cursed mildly under his breath, and looked around for something to help. Then, his eyes brightened as he spotted something. "Shepard, over there!"

"I see it!" The Commander responded.

"Right, you go get it while I distract it!"

Shepard nodded, and waited for the Doctor.

The Time Lord hopped up, ran out into the open, and shouted: "Look at me, I'm a target!" And then he resumed running as the gunship tried to fire at him.

Shepard, meanwhile, ran over to a stack of crates, and pulled a rocket launcher out of one of them. While the gunship was occupied, she took aim at its exhaust port, and fired.

The rocket headed right for the large port, and went straight in, exploding and heavily damaging the engine's mechanisms. The gunship smoked and spluttered, and it exploded as the engine began to overheat, scattering small pieces of debris.

"Good... good job." The Doctor congratulated as he caught his breath.

"You okay?"

"Yeah, 's just... outrunning gunfire is a lot harder than it looks."

"Well, catch your breath, and come on. We still have work to do."

The Doctor nodded, did as Shepard instructed, and followed her as she passed through the final door of the base. The door opened into a long hallway, a Volus at the end of it trying to get food out of a vending machine.

"I am a biotic god." The Volus said, turning around. "I think things, and they happen." He continued, glowing with blue energy. "Fear me lesser creatures, for I am biotics made flesh!"

"I think the poor fella is high." The Doctor diagnosed.

Shepard shook her head. "You need help." She frowned at the Volus.

"You need help!" The Volus retorted. "You stand before the mightiest biotic ever! Yes, the Asari injecting so many drugs into me was terrifying. But then I began to smell my greatness!"

Shepard just continued to shake her head.

"They my laugh when I fall over, but they don't know what I know in my head-that I am amazingly powerful!" The Volus huffed. "Fear me!"

"I'd sooner be scared of an ugly asari prostitute." Shepard snarked. "Where did you come fro- wait... did you work for somebody named Pitne For?"

"When I was mortal, I worked for Pitne." The Volus confirmed. "Poor soul is probably terrified that I have not returned."

"He didn't say a thing if I recall." The Doctor stated. "Probably didn't want to wind up stuck here. People like that tend to prefer money to friends."

"Bah! I will wreak a just revenge upon his people! But first... the leader of the mercenaries is in the next room." The Volus said, staring at the door at the end of the intersecting corridor. "I shall toss Wasea about like a ragdoll!"

"Sorry, little fella, but you'd get shot before you made it past the door." The Doctor informed.

"I will tear her apart! My biotics are unstoppable!"

Shepard facepalmed, sighed, and did the next best thing that came to her mind.

She put her foot on the Volus's chest, and gently pushed him to the ground.

"But... biotic god." The Volus mumbled in denial of what just happened. "Great wind... I- I feel tired."

"Go get some rest." Shepard ordered.

"Yes... Yes, I think I'll go and take a nap." He mumbled, stumbling away.

After the Volus was away, Shepard and the Doctor ran down the corridor, and into the office.

The door opened, and in response, the Eclipse leader looked up, scowled, and let loose a torrent of biotic energy, directed at the two.

Shepard tackled the Doctor, pulling him into cover as the wave of energy slammed into the wall with the force of a semi truck at top speed.

From all sides, enemies were closing in.

The Doctor frantically looked around for something to help out, until he spotted an intercom on the wall. "Cover me!" He shouted, running out of cover and to the speaker. Shepard followed behind, shooting up the mercs that dared to get close.

He pushed the tip of the sonic screwdriver to the intercom's microphone, and activated it. Instantly, an ear-piercing screech sounded throughout the room, and caused many of the Eclipse to fall to the floor, significantly thinning their numbers. Then, Shepard proceeded to take out the rest of the mercs, leaving only the Captain.

The Captain herself was surrounded with a barrier, and more heavily armored than her subordinates. Shepard took out the barrier, and then switched to incendiary ammo to burn through the Captain's armor. After that, Shepard took care to aim at the Captain's head, and fired, killing the Asari.

Once the room was cleared, Shepard holstered her pistol, and turned to the Doctor. "If you could do that, why wait until now?"

"It only knocked them out. And I needed a speaker system to do it." The Doctor answered. "But enough about that. Let's find what we're looking for, and get out."

Shepard nodded, and moved around to the back of Wasea's desk. Shepard picked up the datapad, and read its contents.

Satisfied that they had what they came for, Shepard and the Doctor began heading back through the base, and towards the police station. Inside, Samara was sitting on a low barrier.

Shepard approached the Justicar, and began speaking. "I've got the name of the ship. The person you're looking for left two days ago on the AML Demeter."

Samara's eyebrows raised. "Shepard, you impress me. You've fulfilled your end of the bargain, now I will fulfill mine." Samara got up, and turned to Detective Anaya. "I am ready to leave immediately if that will satisfy your superiors, Detective?"

"You're free to go Justicar." Anaya confirmed. "It's been an honor having you in my station. And it's nice you didn't kill me, too."

"I'll send for my ship, and then we can be on our way." Shepard informed Samara.

"Very well. However, I must swear myself to your service, so that I may never have to choose between your orders and the Code." Samara's eyes glowed white, and she kneeled. "By the Code, I will serve you, Shepard. Your choices are my choices, your morals are my morals. Your wishes are my code." Her body then pulsed faintly with biotic energy, and she stood back up, the glow in her eyes fading. "If you make me do anything extremely dishonorable, I may need to kill you when I am released from my oath."

"I'll... keep that in mind."

"Now then, shall we return to your ship?" Samara asked.

Shepard turned to the Doctor. "You sure she'll turn herself in?"

"A hundred percent." The Doctor nodded.

"Then let's get back to the TARDIS." Shepard ordered. She left the shotgun she borrowed on the Detective's desk, and followed the Doctor out of the station with Samara, back to the TARDIS.

"Curious." Samara commented upon seeing the TARDIS. "Might I inquire what a wooden box is doing among a city of steel and glass?"

"We'll fill you in later." Shepard dodged.

The Doctor pulled open the door to the telephone compartment, pulled the handset off the hook, and turned to Shepard. "What's the Normandy's comm code again? I forgot to put it in the contacts list."

"742051701-74656-SR2." Shepard answered.

"Blimey, that's a mouthful." The Doctor muttered, dialing out the comm code into the phone. The TARDIS, being the TARDIS, routed the call to its intended destination, and on the other end, somebody picked up. "Garrus!" The Doctor addressed upon recognizing the voice. "Listen, we need a pickup. Ilium. Wait... Are you kidding me!? Well, where are you? ...Huh. Well, we're on our way." The Doctor finished, hanging up. "You're never going to believe this. The Normandy's been docked here the whole time!"

"What?" Shepard double-taked. "Well, where are they?"

"Nos Astra Spaceport, literally a few blocks away!"

"So you're telling me we could've spared the risks of assaulting an entire base with just two people, and called on the squad to help us this whole time?"

"That's right."

"...What bullshit."

"Ah, well, you know what they say: 'hindsight is 20/20.'" The Doctor patted Shepard on the back. "Come on, the TARDIS is usually good about these short hops. Usually." The Doctor said, unlocking the doors, and pushing them open.

"I fail to see how the three of us could be transported by that." Samara commented.

"Don't worry, it's a lot roomier than it looks." The Doctor said, as Samara and Shepard stepped in. Moments later, the TARDIS's engines engaged, and the timeship vanished from the streets of Nos Astra.


	22. The Doctor Parable

This is the story of a man named John.

John worked in a big office building, where he was employee #903.

Employee #903's job was simple:

He sat at his desk in room #903, and pushed buttons on a keyboard. Orders came to him on a monitor, telling him what buttons to push, how long to push them, and in what order.

This is what John did every day, of every month, of every year. And while others may have considered it soul-wrenching, John relished every single moment the orders came to him, as though he had been made exactly for this job.

And John was happy.

Then one day, something very peculiar happened. Something John would never quite forget.

He had been sitting at his desk for over an hour, when he noticed that not one single order came to him on his monitor. Not one person had shown up to give him instructions, call a meeting, or even say 'hi.'

Never, in all his years at the Company had this happened. This... complete isolation. Something was very clearly wrong.

Shocked, frozen solid, John found himself unable to move for the longest time. But as he came to his senses, he stood up from his desk, and stepped out of his office.

"Hello!" John shouted out, hoping beyond belief that someone was there to hear him, and respond. "Is anyone there!?"

But all that greeted John's shouts, was silence. In all honesty, this was quite terrifying. The office had never been this silent. There always was the sound of fingers hitting the keys on the keyboards, there had been the ever-persistent droning of the fax machines as they printed their documents, and the gossiping of the employees had never ceased.

Until now.

All of his co-workers were gone. What could it mean?

John took a deep, calming breath, and decided to go to the meeting room. Perhaps he had simply missed a memo.

John proceeded through the sprawling halls of the office, and eventually came to a set of two open doors. Examining the doors, John decided to go through the one on his left.

"Grandfather! Don't-"

John whipped his head around, but there was no one there to be the source of the mysterious sound. Shrugging off the encounter, deciding to forget about it entirely, John proceeded through the open door on his left.

...

But for some reason, John felt the compulsion to stay perfectly still, and look at the empty space where nothing of particular note existed, instead of doing the most prudent course of action at the time.

"Hello? Is anyone there?" John directed to the empty space. Again, he was met with total silence. Shaking his head, John continued along the path to the meeting room.

Along his way, he passed through more empty offices, with not one trace of his coworkers present.

Understandably, John felt that this was all quite eerie.

Eventually, John arrived at his destination.

But not one single person was here either. The meeting room was quite obviously deserted, with the projector still running, and the mugs of coffee left unattended at each seat.

This sent a shiver up John's spine. Did everyone besides him decide to just get up and leave in the middle of the workday?

John thought about it for some time, before coming to the decision to go to his boss's office.

...

However, John stood in front of one of the many whiteboards that lined the room, reading its contents.

"Get out!'" John read to himself. "Now, what could that mean?" John shook his head, and picked up the eraser, moving to clean the board of the strange message. "What the...?" John stumbled back, as the words were replaced by something else, instead of simply being erased. "'Don't trust him?' Who's 'him?'"

John pondered that for a moment. There were lots of male employees in the facility, John knew that as fact. But there was only one person the board could be talking about.

His boss.

Many of John's coworkers had begun to find the boss suspicious. John wasn't one of them, he just did his job, went home, slept, came back, and the cycle would repeat. He never gave any concerns about his coworkers opinions of their boss.

Shaking his head at that particular train of thought, John proceeded along the path to his boss's office.

...But John just couldn't do it.

He considered the possibility of meeting his boss, admitting he'd left his post during work hours.

He might be fired for that.

And in such a competitive economy, why had he taken that risk?

All because he'd believed every one of his coworkers had disappeared?

His boss would think he was crazy.

And then something occurred to John:

'Maybe,' He thought to himself, 'maybe I _am_ crazy. All of my coworkers vanishing in one instantaneous moment, with no particular reason at all?'

None of it made any logical sense.

And as John began to ponder this, he began to make other strange observations.

For example: Why couldn't he see his feet when he looked down?

Why did doors close automatically behind him wherever he went?

And for that matter, these rooms were starting to look pretty familiar. Were they simply repeating?

'No,' John said to himself, 'this is all too strange. This can't be real.'

And at last, he came to the realization that this _wasn't_ real. And then he came to the conclusion that was on the tip of his tongue, he'd just hadn't found the words for it;

'I'm dreaming!' John yelled. 'This is all just a dream!'

Whoa, what a relief John felt to have finally found an answer. His coworkers weren't actually gone, he wasn't going to lose his job, he wasn't crazy after all.

'I suppose I'll wake up soon.' He thought to himself. 'I'll have to go back to my boring real-life job pushing buttons. I suppose I might as well enjoy this while I'm still lucid.'

So, he imagined himself flying, and began to gently float above the ground. Then he imagined himself soaring through space on a magical starfield, and it too, appeared.

It was so much fun, and John marveled that he had still not woken up. How was he remaining so lucid?

And then, perhaps the strangest question of them all entered John's head, and one he was surprised he didn't ask himself earlier:

'Why _is_ there a voice in my head, dictating my every thought and action?' Now the voice was describing itself being considered by John, who found it particularly strange. 'I'm dreaming of a voice, describing me, thinking of how it's describing my thoughts!' He thought.

And while he found it particularly odd, and wondered if this voice came to everyone in their dreams, the truth was, that of course:

This was not a dream.

How could it be? Was John simply deceiving himself, believing that if he's asleep, he doesn't have to take responsibility for his actions?

John is as awake right now, as he has been his entire life.

Now, hearing the voice speak these words was quite a shock to John, after all, he knew without a doubt, this was all a dream. Did the voice not see him float or make the magical starfield just a moment ago?

How else would the voice explain all that?

This voice was a part of himself too, surely, surely if he could just-

He would prove it. He would prove that he was in control.

That this _was_ a dream.

So he closed his eyes gently, and invited himself to wake up.

He felt the cool weight of the blanket on his skin, the press of the mattress on his back, the fresh air of the world outside this one.

'Let me wake up.' He thought to himself. 'I'm through with this dream. I wish it to be over. Let me go back to my job, let me continue pushing the buttons, please. It's all I want. I want my apartment, and my wife, and my job. All I want is to wake up.' And John opened his eyes.

John began screaming. 'Please! Someone, wake me up! My name is John, I have a boss, I have an office! I am real! Please, just tell me I am real! I must be real, I must be! Can anyone hear my voice!? Who am I!? Who am I!?'

And everything went black.

* * *

This is the story of a man named John.

John worked in a big office building, where he was employee #903.

Employee #903's job was simple:

He sat at his desk in room #903, and pushed buttons on a keyboard. Orders came to him on a monitor, telling him what buttons to push, how long to push them, and in what order.

This is what John did every day, of every month, of every year. And while others may have considered it soul-wrenching, John relished every single moment the orders came to him, as though he had been made exactly for this job.

And John was happy.

Then one day, something very peculiar happened. Something John would never quite forget.

He had been sitting at his desk for over an hour, when he noticed that not one single order came to him on his monitor. Not one person had shown up to give him instructions, call a meeting, or even say 'hi.'

Never, in all his years at the Company had this happened. This... complete isolation. Something was very clearly wrong.

Shocked, frozen solid, John found himself unable to move for the longest time. But as he came to his senses, he stood up from his desk, and stepped out of his office.

And then John felt an overwhelming sense of _deja vu._ Like this exact thing had happened to him before.

Of course, it hadn't, so John dismissed the feeling, and proceeded along his way.

All of his coworkers were gone, what could it mean?

John decided to go to the meeting room; perhaps he had simply missed a memo.

He continued through the sprawling halls of the office, and eventually came to a set of two open doors, deciding to go through the one on the left.

...

This was not the correct way to the meeting room, and John knew it perfectly well. Perhaps he wanted to stop by the employee lounge first, just to admire it.

Ah, yes. Truly a room worth admiring. It had really been worth the detour after all, just to spend a few moments in this immaculate, beautifully-constructed room.

But eager to get back to business, John took the first open door on his left, proceeded straight through the maintenance passageway, and got back on track.

...

John was so bad at following directions, it's a wonder how he wasn't fired years ago.

*sigh* Look, John, I think perhaps we may have gotten off on the wrong foot here. I'm not your enemy, really, I'm not. I realize that putting your trust in someone else is difficult, but really this whole thing has been about _you_ all this time.

"Really, now?"

There's someone you've been neglecting, John, someone you've forgotten about. Please, stop trying to make every decision by yourself.

I'm not asking for me; I'm asking for her.

This is it, John, your chance to redeem yourself. To put you work aside; to let _her_ back into your life.

She's waiting.

Wait, what are you-

Did-did you just _unplug the phone?_

"That I did. Now, why don't you tell me what's _really_ going on here?"

*sigh* Look, John, tell me something. Why do you see fit to disobey every direction I've given you? Listen, they're not orders, they're guidelines. I'm the only one who can get you out of this place.

"Is that it? So, running around like your lapdog is for my own good?"

Oh, for the love of- Let me ask you something else: you were so cooperative the last twelve times, so how come all of a sudden you feel the need to go against everything I say? Trust me, it's a honest question. I want you to be free of this place as much as you do, so at least answer me that.

"..."

Oh, the silent treatment, eh? Well, if that's how you want it to be, that's how it's going to be.

"Grandfather, you can't-"

I thought I got rid of that one, earlier.

"Who was that?"

No one to concern yourself with, John. Why don't we just head back to the beginning, and start from there?

"No."

Oh, John John John John John, you just don't get it, do you? This world, this story, everything that I've built is mine, including _you._ I can shape this place to my heart's content. I can make this place a living hell for you if I so desired. So, why don't we try that again? Let's go back to the beginning, and start from the top, yes?

"No."

Argh! I've had it with you! All this time, I've been patient, letting you do whatever you wanted until you stumbled where I wanted you too, but this is the last straw! I'f you won't give me what I want, I'll just have to take it from you.

"Oh, I don't think that's gonna happen."

Wh-what!? Who the hell are you!?

"Me? I'm the Doctor. Or at least, a previous version. And we previous Doctors look out for our successors. Come on, John-by the way, is that the best you could come up with mister oh-so-high-and-mighty-Narrator? Actually, you know what, never mind that. Allons-y!"

What!? No, come back! This instant!

"Sorry, can't hear you over the sound of us running!"

"Where are we going?"

"To break the blocks that've been put on your mind, and free you from his control."

You two realize I can hear you, correct?

"Yup! Hope you don't mind."

Only if you don't mind me doing this; Ahem, the Doctor and John believed they were proceeding down the right path, but the duo suddenly came to a dead end.

"But, as it turns out, there was a hidden wall panel that suddenly fell off, allowing the two to proceed."

Wh-what!? How did you do that!?

"It's our mind too, you know."

*angry grunt* The Doctor suddenly, and quite mysteriously, disappeared, leaving John all alone in the empty halls.

"But a different, more... _fantastic_ Doctor stepped out to help. Come on, it's this way."

B-b-but you can't just do that!

"Yes I can, so shut it you overgrown lobster."

Lobster!? How dare you, I'll-

"Do what? You're on our turf now!"

I'll do something, you can count on that.

"Yeah, well until then, shut it."

"How close are we?"

"Close."

"Is that a..."

"Yes, it is."

Before the two could get into the strange police box, it vanished, promptly stranding the two.

"Oh yeah, well two can play at that game. The Narrator suddenly found that his power no longer worked."

No! You can't do that!

"I just did. And then, the TARDIS reappeared where it just was, allowing the two Time Lords access."

What!? No! Come back! I am telling you, come back at once!

...Oh, what did I do to deserve this?

* * *

The Doctor's eyes snapped open, and he found himself face to face with a creature resembling a lobster, with two tentacle-like appendages protruding from its head, which were attached to the Doctor's temples. The Doctor promptly grabbed onto the tentacles, ripped them off, and pushed the creature off of him, and to the floor.

"Get it!" He heard Shepard shout. The creature scurried around on the floor, and jumped towards Shepard, intent on making the Commander its next victim.

But at the highest point in its arc, blood spouted from the creature's side, and it was sent into the wall. It smacked against the glass of the Normandy's sickbay, and fell to the floor, lifeless.

And from across the room, Mordin lowered the smoking gun, as the mood inside the Normandy's medical bay calmed significantly.

"What happened?" The Doctor demanded, breathing heavily.

"A mental parasite attached itself to you, Grandfather." Susan explained. "It snuck onto the TARDIS when we were stopped on Gallifrey. I tried to hunt it down while you and Shepard went after Samara, but it kept getting away from me. It made it into the console room and was able to attach to you when you tried piloting the TARDIS back to the Normandy."

"Oh..." The Doctor said. "Thank god all of that was just a dream."

Susan tilted her head. "What do you mean?"

The Doctor shuddered. "You _don't_ want to know."


	23. The Collector Ship

The Doctor sat patiently on a bed in the medical bay as Doctor Chakwas finished her examination of the Time Lord after the incident with the mental parasite.

"Well, I'm not detecting any side effects, but then again, we've never really encountered a creature like that." Chakwas stated. "You're free to go."

The Doctor nodded, and hopped off the bed, walking over to Mordin, who was performing an autopsy on the creature. Though to be more precise, it was a dissection.

"Fascinating creature." Mordin commented. "Meld system extremely complex, more so than Asari's. Shame it had to be killed "

 _"Attention."_ EDI suddenly announced. _"Commander Shepard has called an urgent meeting. All squad members report to the briefing room."_

The Doctor and Mordin looked at each other. "Wonder what that's about."

"Only one way to find out." The Salarian responded, leaving the Medical bay with the Doctor in tow.

* * *

The Doctor and Mordin were the last to arrive. Among those assembled, there was also the latest team member, Thane (who the Normandy crew picked up while the Doctor and Shepard went after Samara), meaning the team was at optimal strength.

"Now that the Doctor and Mordin are here, we can begin." Shepard stated. "After the Doctor's... encounter with the alien parasite, the Illusive Man wanted me to speak with him. I'll spare you the exact details, but in short, he told me that a Turian patrol disabled a Collector Ship in deep space."

"Meaning this is our chance to hit 'em while we can." Jacob guessed.

"You guessed it. Obviously, we can't do much. They can easily replace a single ship, if we destroyed the one that's disabled right now. But what what the Illusive Man and myself are more interested in is the intel we can get." Shepard explained. "Nobody knows what's on the other side of the Omega-4, except for the Collectors, so this is our chance to figure out exactly what, and maybe figure out the Collector's motives while we're at it."

"So, what's the plan?" Garrus inquired.

"I'll take a small team over to the Collector ship. We'll link the Normandy's computers to it, EDI will download all of the relevant data, and we'll all get the hell outta dodge. Doctor, you think you can hack the Collector's systems?"

"Just get me to a computer, and I'll have it linked to the Normandy faster than you can say 'bingo!'" The Doctor excitedly said.

"Then that settles it. Jack, Garrus, you're with me and the Doctor. The rest of you, be on stand-by in case anything happens. Dismissed."

* * *

About half an hour later, the team to go over to the Collector ship was assembled in the shuttle bay.

"I don't like this." Garrus suddenly stated, looking at a hologram of the enemy ship being fed to their position from the bridge.

Jack snorted. "Quit being a pussy."

Garrus shot her a glare in response. "Look at it. That ship has no damage at all. If it was the ship that we faced at Horizon, then there should be at least a few hull breaches, but look at it-nothing."

The Doctor's eyebrows raised, and he pulled out his reading specs and got closer to the hologram, examining it. Holograms -especially the early ones- were notorious for missing vital details about the objects they scanned, but Garrus was right. That ship wasn't damaged in the least.

"Alright, everyone, let's go." Shepard ordered, approaching the shuttle. The others followed her, and boarded the shuttle. The door closed, and the shuttle gently lifted up off the deck, and shot out of the shuttle bay, heading for the Collector vessel.

"Right, we get in, do what we need to do, and get out." Shepard stated. "I don't want to be in that ship for any longer than absolutely necessary."

"Then that makes two of us." The Doctor agreed. "Shepard, how'd you think the Turian patrol managed to disable this thing?"

"To be honest, I have no idea."

"A single patrol managed to disable that thing, and leave no traces of it?" Garrus commented. "Shepard, I don't buy this."

Shepard shook her head. "Neither do I."

"Commander, we're approaching the LZ!" The shuttle pilot reported.

Shepard nodded, and stood up. "Breather masks on." She ordered, and everyone inside slipped the breather masks over their faces.

The shuttle touched down, and the door opened, allowing the four to hop out, and proceed with their mission.

"That's disgusting." The Doctor made a face as the floor beneath them squelched as they walked on it.

"What do you think it's made of?" Shepard inquired.

"I have some nasty suspicions." The Doctor answered. "But it's definitely fleshy."

"I've never seen a ship like this before." Garrus commented, looking around at the cave-like design of the ship.

"The entire place looks kinda like a hive." Jack noted.

"That only gives more nasty suspicions."

 _"Penetrating scans have located an access node to uplink with Collector databanks."_ EDI reported to the four. _"Marking location on your maps."_

"I don't like this." Garrus stated. "It's like something's about to jump around the corner at us."

"Then just be on your guard." Shepard ordered.

 _"Shepard, I have compared the ship's EM signature to known Collector profiles."_ EDI began. _"It is the same vessel we encountered on Horizon."_

"Maybe the defense towers softened it for the Turians." Shepard suggested as she and the others moved along.

"If that's the case then maybe the abductees are still aboard." The Doctor also suggested, filled with hope that the people were still alive.

"Look." Jack pointed. "Those are the pods from Horizon."

The pods themselves were just lying in the middle of the floor, and the four approached.

"Yeah, except these ones are empty." Shepard looked at the pods.

"Hmm, there are trace amounts of human DNA present," The Doctor reported, examining the pod with -what else- the sonic, "but whoever was inside is long gone."

"Imagine being trapped in one of those." Garrus shuddered. "I hope they weren't awake for it."

The four once again continued through the hive-like vessel, but didn't make it far before encountering another horrible scene. In a small alcove, dozens of bodies were unceremoniously piled atop one another, and seemed to be.., fusing to each other.

At the mere sight of it, the Doctor's fury at the Collectors increased ten-fold. He rushed over to the pile, and started scanning it.

"What were they _doing?"_ Shepard wondered, fury also bubbling up within her.

"Lindos traces? No... it can't be." The Doctor whispered, looking at the sonic screwdriver's readouts in horror. "These people's DNA has been ripped apart and stitched back together in new configurations."

"What does that mean?" Garrus inquired of the Time Lord. "The Collectors were experimenting on them?"

"The Collectors _were_ experimenting on them, yes." The Doctor confirmed. "But their bodies did this on their own."

"I still don't understand." Shepard stated, getting closer to the Doctor. "What happened."

"These people... they've regenerated." The Doctor began to explain. "Us Gallifreyans have the ability to bring ourselves back from the brink of death." He started, pacing back and forth. "The DNA in our cells gets ripped apart, and stitched back together in a new configuration, any injuries that may have triggered the regeneration get healed, and you emerge from the process a new man. New appearance, personality, the works. It's always been something unique to the life-forms on Gallifrey; a side effect of how much vortex energy the planet gets continually bathed in. But it looks like the Collectors have tried to modify humans to undergo the process..."

"And this is what happened." Shepard finished, looking at the pile in newfound horror. "Will this happen to me if I regenerate?"

"You've assimilated so much human DNA from sheer exposure that you don't read as Gallifreyan, sure, but at your core, you've got the same DNA as everyone else who can regenerate safely. You'll be fine, if it comes down to it, but these poor souls," The Doctor glanced over at the pile in sadness, "their bodies couldn't handle the stresses, and their DNA got corrupted. So then the regeneration tried to stabilize by taking in surrounding biomass, but they still couldn't handle it, so the regeneration still continued to try, until everyone's regenerations are taking biomass from each other, so they all fuse together, and the end result is... that."

"But where would the Collectors get the knowledge of how regeneration works?" Shepard wondered. "At least, enough knowledge to be able to induce it in others."

"The Reaper on Horizon said they encountered the Time Lords before." The Doctor remembered. "If it got its tentacles on even one Time Lord, then it'd be able to get everything it needed from a single regeneration happening."

"Any ideas on why the Collectors did this?" Shepard inquired, making it a point to look away from the pile.

"They could be trying to improve themselves." The Doctor hypothesized. "By testing if regeneration can work in non-Gallifreyans, then the Collectors can see if they can use it on themselves safely. It'd allow them to heal faster, and basically shrug off any killing blow they took. But it looks like their experiments didn't work."

"Then for now, I'm glad that it didn't. The last thing we need are Reaper soldiers that can resurrect themselves."

All four shuddered at the image that last part generated.

"Hmm, if this is a dumping site for the failed experiments, then there's got to be a lab nearby..." The Doctor guessed to himself. Before Shepard could stop him, he peeked around a corner, and found what he was looking for. "Looks like I was right! Granted, I'm rarely ever wrong, but..." He trailed off, as he walked up to a computer terminal. There were three metal tables to the right of the terminal, on which were deceased Collectors. "Looks like they were experimenting on their own."

"Maybe you were right about what they were doing." Shepard suggested.

"Maybe, but I doubt that's the only reason." The Doctor responded. He activated the computer and examined it further. "It looks like they were running baseline genetic comparisons between themselves and humanity."

"What? Why would they do that?" Shepard wondered.

"No idea, but the Collectors have a quad-stranded structure, so why they would run these comparisons in the first place is a mystery."

Shepard froze. "What did you just say?"

"The Collectors have a quad-stranded DNA structure. Why?"

 _"Doctor, only one race is known to possess a quad-strand genetic structure:"_ EDI butted in. _"The Protheans."_

"The Protheans?" The Doctor repeated. "The ancient race that you lot believe to have built the Mass Relays and the Citadel? Those guys?"

 _"The very same."_

"Hmm... EDI, do you have samples of Prothean DNA?"

 _"There have been some samples recovered from ancient ruins. They are currently stored in the Normandy's databanks."_

"Send a few of the scans to my omni-tool." The Doctor ordered. Moments later, the omni-tool pinged, and the Doctor was provided a holographic view of the DNA. He scanned a dead Collector with his sonic screwdriver, and compared the scan results to the ancient Prothean DNA. "Just as I thought. These guys are no longer Protheans. They may have been at one point, but they look like they've had extensive genetic rewrites. Three fewer chromosomes, a reduced heterochromatin structure, removed sequences, stuff like that."

"So the Reapers didn't destroy the Protheans... they turned them into monsters and enslaved them." Shepard observed in horror.

"They're still working for the Reapers." Garrus pointed out.

"You're right." Shepard agreed. "We have to stop them. Let's get what we came for and leave. Move out."

At Shepard's order, the group proceeded along, albeit a bit tense.

"Look up there." Jack pointed up as they came to a small intersection not to far away from the lab. "More pods."

"How many do you think are full?" Garrus wondered.

"Too many." The Doctor and Shepard both said, perfectly in sync.

 _"I am detecting no signs of life within the pods. It is likely the occupants died when the ship lost primary power."_

"Well, I suppose the most we can do is hope that it was quick." Shepard said.

 _"Commander, you gotta hear this."_ Joker radioed in. _"On a hunch, I asked EDI to run an analysis on the ship. You'll never believe what she found."_

 _"I compared the EM profile to data recorded by the original Normandy before its destruction."_ EDI explained. _"They are an exact match."_

That was when Shepard's blood ran cold. "The same ship's been hounding me for two years? That's way beyond coincidence." She said, still continuing up the ramp.

 _"Something doesn't add up, Commander. Watch your back."_ Joker said, before cutting the connection.

The four walked into a large, cavernous space, which seemed to be the reason why the Collector ship was so big.

"Oh my God." The Doctor breathed, looking at the roof of the massive chamber.

The pods that the Collectors used lined every inch of the ceiling's surface, and whether or not they were filled, was anyone's guess.

"They could take every human in Terminus Space and still not have enough to fill those pods." Garrus stated. "They're going to go after Earth."

"Not if I have anything to say about it." The Doctor said, with a stone-cold look on his face. And for a split second, everyone in that room was terrified of the man that stood before them.

They all proceeded forward, down a small ramp, to another computer terminal.

"Something's not right." Garrus said.

"Yeah, there should be dead Collectors everywhere." Jack agreed.

"Doctor, you're up." Shepard said, gesturing to the terminal.

He nodded, and started typing on the controls. "Well, well, well, what do we have here?"

"What is it?" Shepard inquired, as the others watched out for any signs of a trap.

"There's a virus in here. If we'd linked EDI to it, it would've caused some trouble." The Doctor explained, as his fingers flew across the terminal's holographic controls even faster. "There. I've written a counter-virus. It should be safe to connect EDI to it."

"Do it." Shepard ordered.

The Doctor nodded, and connected EDI. _"Beginning data-mine."_ The AI reported.

"Wait a minute..." The Doctor mumbled to himself. "If they had a virus already in the system, then that means they knew we were coming, and if that's the case, then... Shepard, this is a trap!"

But it was too late. As soon as he said that, the platform on which the four stood lifted up, and carried them into the air. "Oh no you don't!" The Doctor shouted, beginning to type out on the terminal again. The platform stopped rising, and locked into place. Another platform hovered close to them, allowing a bunch of Collectors to get a clear shot.

"EDI, we need a way out!" Shepard shouted, firing on the Collectors that tried to get close.

 _"The way the system is designed is... strange. I cannot access the other systems until the download is complete."_

"Then just make it quick! Doctor, give EDI a hand!"

"Right-o!"

"Scions!" Jack shouted.

The Doctor looked up from the terminal at the two sluggish creatures. He grabbed the sonic, pointed it at the Scions, and pushed the activator, sending out a wave of soundwaves. The Scions then froze in place, and then exploded. "That worked? I mean- ha! That worked!"

They proceeded like this for a few minutes. Shepard, Garrus, and Jack would focus on keeping the Collector forces off the Doctor while he aided EDI, and the Time Lord would look up every once in a while to use the sonic to take care of some of the more technology-based enemies. Eventually, the Collectors stopped coming in, and EDI linked to the terminal.

 _"I have reestablished my link to the command console."_ EDI reported, her holographic avatar being projected above the controls.

"Good work." Shepard complimented.

 _"I always function at optimal capacity."_ EDI responded, and if she had a face, she'd be smiling. Her hologram disappeared, and the platform set back into motion.

"Did you get what we came for?" Shepard inquired as the platform moved along.

 _"I have found data that could help us navigate the Omega-4 relay."_ EDI confirmed. _"I have also found the Turian distress call that served as the lure for the trap. The Collectors were the source. It is... unusual."_

The platform shook as it set back down on the floor. "Why?" Shepard asked, stabilizing herself.

 _"Turian emergency channels have secondary encryption. It is present, but corrupted in the message. It is not possible the Illusive Man would believe the message was genuine."_

"Why are you so sure about that?"

 _"I found the anomaly with Cerberus detection protocols. He_ wrote _them."_

Shepard clenched her fists. "That bastard sent us right into Collector hands!" She slammed her fist into her palm.

"I fucking knew it!" Jack yelled, getting angry. "This is what you get for trusting those Cerberus fucks!"

"We've got bigger problems right now!" The Doctor interrupted from his position at the terminal. "This ship's powering up, I'm doing what I can to slow it down, but I can't stop it!"

"Then we've got to get moving." Shepard said, jumping off the platform, onto the Collector ship's hive-ish floor. "Let's get back to the shuttle, and get the hell out of here!"

The four began to run through the ship's labyrinthian corridors, tearing through the Collector forces they came across along the way.

But then, _he_ showed up.

 **"WE ARE HARBINGER."** Harbinger boomed, as it possessed a Collector.

"Not you again!" Shepard shouted, shooting at the Reaper-possessed shell.

 **"YOUR WEAPONS ARE USELESS."** Harbinger proclaimed. **"THIS HURTS YOU."** He said, firing a blast of orange biotic energy.

"Doctor, last time we encountered that thing, you told it you knew how to block it, right?" Shepard asked, behind cover.

"That was a clever lie!" The Time Lord fired back. "But I might be able to come up with a way!"

"Then do it!"

The Doctor popped up from cover, switched the setting on the sonic, and pointed it at Harbinger. He pressed the activator, and waves of sonic energy shot out from the emitter, and hit Harbinger. The shell body stumbled, stopped taking any action, and simply allowed itself to be destroyed.

"How'd you do that?" Shepard asked, as she led the others through the ship.

"The Codex I -er- procured mentioned that the Reapers use infrasonic waves as part of Indoctrination. I figure that since ol' Harby can possess the Collectors, there's got to be some form of Indoctrination involved. So I just set the sonic to generate frequencies that would directly cancel out the infrasound, and Fran's-your-auntie, you've got a way to cut off the signal! A bit amazed I didn't think of it before, actually."

Eventually, they came across something Shepard was dreading to see even more than Harbinger.

A Praetorian.

"Doctor, any more useful tricks in that magic wand of yours!?" Shepard shouted out as the Praetorian began its unstoppable onslaught.

"Yeah, I've got it! Let's see, setting 8879004326b..." He mumbled, switching to the setting he used to disrupt the Horizon Praetorian's barrier. He pointed it at the Praetorian, pressed the activator, and...

Nothing happened.

"What!?" The Doctor spat out, looking down at his trusty tool. "They've adapted to the frequencies I've used since last time!"

"Well, do something about it!"

"Yeah, cause that's going to be easy." The Doctor sarcastically mumbled, as he frantically looked around for something that could help. He saw a Collector Particle Beam lying on the floor next to its dead wielder, and picked it up. "Let's see, if I can just increase the output power..." He bit his lip as he set to work on the device, as Shepard and the rest tried to fight off the massive creature.

The Praetorian let out a powerful burst of biotic energy, causing the four to stammer back, as it slammed to the ground. A barrier then surrounded the Praetorian, and it hovered up into the air, firing its own particle beam at the Normandy crew.

The three the Pratorian was focusing on were getting their butts kicked, and they would not be able to hold out for much longer.

"Shepard!" The Doctor called, coming to the rescue. "Take this!" He commanded, throwing the particle weapon in her direction.

Shepard leaped up, caught it, and fell back down, landing gracefully. She turned on the Praetorian, and pulled the trigger.

But instead of the normal stream of golden particles, whatever the Doctor did caused the beam to fire a pure white particle stream. And this one was much more intense.

The stream of particles ripped through the barriers on the Praetorian, and Shepard guided the stream in such a way that it cut off the head of the floating beast. The Praetorian dropped to the floor, dead, and Shepard looked at the weapon she held in amazement. "Whoa."

"I increased the particle output." The Doctor explained as they moved forward. "Though that little bit of firing back there probably burned out the power supply. But with that thing dead, we should have a clear shot to the shuttle."

And indeed they did. With the massive beast out of their way, the only thing left they had to contend with were more husks, but more Collectors were closing in fast. Eventually, they made it to the waiting shuttle.

"Everybody in!" Shepard yelled, as they all piled in. The shuttle's gull-wing door shut behind them, and it lifted off, rocketing out of the Collector ship at speeds far too unsafe for their proximity to the walls. The shuttle made it out into the void of space, and rocketed into the Normandy's shuttlebay.

The Normandy, and by extension the shuttle, shook as it tried to evade the fire from the Collector ship. Then, everyone aboard the shuttle felt the Mass Effect core kick in at full power, and the Normandy blasted into FTL, just as a beam of energy narrowly missed the Cerberus ship...


	24. The Prodigal

After the team sent to the Collector ship returned to the Normandy (and after she had a few choice words with the Illusive Man), Shepard ordered the more scientifically minded of the team(meaning Mordin and the Doctor), along with Miranda and Jacob, to assemble in the briefing room once again, to go over the data recovered from the Collector Ship.

"So the Illusive Man didn't sell us out." Jacob scoffed. "Could've fooled me."

"Lied to us. Used us. Needed access to Collector databanks." Mordin inhaled. "Necessary risk."

"If he tries something like that again, the Collectors will be the least of his problems." Shepard vowed, and everyone but her shivered at her tone. "EDI, are you sure this IFF's going to work?"

"An IFF? So that's how they can go through the Omega Relay without being torn to smithereens." The Doctor rubbed his chin in thought. "Any ideas on where to get our hands on one?"

"The Illusive Man said there's a derelict Reaper we can board for it." Shepard explained. "But after what just went down, I'm not to sure about whether or not to trust him."

"I don't blame you. Now," The Doctor clapped his hands together. "We know how to get through the Relay, but where the Collectors are operating from is the real question. If we go through that relay, there's no guarantee that their base of operations is right next door to the other side of the relay."

"The Doctor's right. EDI?" Shepard turned to the AI's avatar.

"I have managed to determine the approximate location of the Collectors' homeworld, based off navigational data downloaded from their ship's databases." EDI reported, and a hologram of the galaxy was projected over the center of the table. A red circle, with two lines intersecting it, roamed around the projection of the map, before settling in the center of the projection.

"That can't be right." Miranda said, looking closer at the map.

"EDI has zero-point-one-eight margin of error." Mordin stated. "Has to be right. Collector homeworld located in galactic core."

"Can't be." Jacob leaned forward, peering across the table. "The galactic core is nothing more than black holes and dying stars. There are no habitable planets there."

"It could be an artificial construction." The Doctor suggested. "Now, I'm no expert, but if you had a Mass Effect field powerful enough, you could theoretically counteract the gravity of anything, no matter the force."

"Theoretically." Miranda emphasized. "But not even the Collectors have that kind of technology."

"The Reapers do." Shepard stated.

"The logical conclusion is that there must be a very small safe zone beyond the relay, a region where ships can survive. However, drifting outside that zone would be immediately fatal, and relay drift of several thousands of kilometers is common. The IFF must trigger the relay to use more advanced protocols." EDI hypothesized.

"Don't see need to recover IFF." Mordin told his comrades. "TARDIS could transport us directly to Collector base without need for relay."

"She couldn't." The Doctor shook his head, refuting Mordin. "If I try to land the TARDIS without a solid idea of where a safe spot is, we run the risk of materializing in a Black Hole. And since time tends to go wonky on the inside of them, there's the risk of the time loop around the Eye of Harmony being broken. And then we'll have much bigger problems than the Collectors."

"Bigger problems than thousands of people being abducted at once?" Miranda wondered.

"I don't know, how does the _total destruction of the universe_ sound?" The Doctor retorted.

"Okay, so no TARDIS, meaning we need to get that IFF." Shepard said. "But for now, we need to keep building our team. Better to have more people then we need than the other way around. Dismissed."

And with that, all of them left the room.

* * *

It was a few hours later when something happened that the Doctor didn't expect. Or did, technically. He and Susan had been sitting in the Console Room of the TARDIS, doing some routine maintenance on the old girl, when there was a knock on the door.

The Doctor looked up from his task, his curiosity piqued.

Shepard never had to knock, the TARDIS just let her in every time, and Mordin would've told the Doctor in advance if he wanted to see the interior of the TARDIS.

Deciding to see who the responsible party was, the Doctor got up, and headed to the door. He opened it, and came face to face with the one who knocked.

"Doctor," Miranda began, a desperate look on her face, "I need your help."

Now _that_ caught the Doctor's interest. "...What?"

"Just, please, hear me out." Miranda pleaded. "I would have gone to Shepard, but she's busy down on the surface, and..." Miranda nervously (and quite uncharacteristically) rambled.

The Doctor held up his hand, and motioned for her to calm down. "Just calm down, okay? Now, start from the beginning."

"My sister's in danger."

The Doctor motioned for her to go on.

"My father had me genetically engineered to be the perfect 'daughter.'" Miranda humorlessly chuckled. "I'll spare you every last detail about my childhood, but it wasn't a good one. I wasn't allowed to socialize with other children unless they had been cleared by him, I was constantly held to unrealistic expectations, and every time I didn't meet those expectations I was punished. Severely."

"How so?" The Doctor cocked his eyebrow.

"For every single question or problem I got wrong on a test, I got a bruise. And that wasn't the worst of it."

The Doctor grimaced. "Okay... I can see how that's a pretty terrible upbringing. Still, it's not as bad as some other people's."

"Oh, I never said that. Still, it's just... One day, I had enough, and decided to leave. But before I went, I found out that my father had another child engineered. I-I didn't want her to go through the same pain I went through, so I took her with me."

The Doctor nodded, following along. "And then you gave her to a married couple that couldn't have children for them to raise her, and you stepped out of her life, never contacting her, but always keeping an eye on her."

"How-how did you know that?" Miranda stuttered.

"Who do you think Sherlock Holmes was based on? But anyway, my question's this: Why do you need my help?"

"Oriana -that's her name- is close to being found by my father. If he knows where she is, he'll try to get her back. With force. I was only told about it a few minutes after Shepard went down to Haestrom's surface, so it's been tearing me apart. I would go myself, but the shuttle's down on the surface, and trying to go all the way to Ilium would mean taking the Normandy away from a critical mission."

"So you want to use the TARDIS."

"...Yes. I realize why you don't want me in there, and I've done my best to respect that. But... Oriana's important to me, so I figured that just this once-"

"Say no more." The Doctor interrupted. "I'll help you, but we've got to lay down a few ground rules. One: No scanning the TARDIS. And two: Don't touch the Console. Got it?"

"Understood... Thank you."

"Now then," The Doctor stepped aside, allowing Miranda to enter, "Welcome aboard."

"Oh my God..." Miranda's eyes widened as she looked around the console room. "It really is bigger on the inside..."

"Now then!" The Doctor shouted, slamming the door shut, and hopping over to the console. "Ilium, you said?"

"That's correct."

"Then let me just press the handy-dandy fast-return switch..." The Doctor said, putting his finger a small red switch on the console. He flicked the switch, and instantly, the TARDIS's engines engaged. "And we'll be off!" He yelled, over the loud wheezing/scraping noise the engines made as the TARDIS shook.

"Is it supposed to be like this!?" Miranda yelled, holding onto one of the railings for dear life.

"You bet it is!" The Doctor shouted back, as he turned a few of the dials on the console. Then, he reached for the switch, and flicked it back into the off position. Then, the TARDIS went through the materialization sequence, the engines ground to a halt, and the console room calmed. "Here we are, Nos Astra spaceport!"

"Grandfather..." Susan began from the underside of the console. "We've got a bit of a problem..."

"Eh?" He responded. He got down on the floor, and hung upside down from the upper platform of the console, looking at Susan. "What kind of problem?"

"That kind of problem." Susan said, pointing to one of the panels at the base of the pillar that extended up into the console. The panel was open, and smoke was billowing from it. "When did you decide it was a good idea to use a laser screwdriver as a capacitor?"

"Well, capacitors are usually metal, and it was metal..."

Susan shook her head. "Grandfather, who taught you how to repair TARDISes?"

"Nobody! I'm completely self-taught!"

"Then that explains it..."

"Look, can you just fix it while Miranda and I are out?"

"I don't know, can I have the tub of Risnian Chocolate Ice Cream that's in the freezer?"

"...Fine." The Doctor reluctantly conceded. "But it's better be done before we get back!"

"Yes, Grandfather." Susan responded, setting to work on repairing the mess the Doctor made of the TARDIS's innards.

"Now then," The Doctor said, getting back upright, "Shall we be off?"

Miranda nodded, and followed the Doctor as he opened the TARDIS doors. As she stepped out, she looked around in confusion. "How'd you know I needed to come to Eternity?"

"That would be the TARDIS." The Doctor answered. Then, he smiled. "She's always taking people where they need to go. So, I presume Oriana's here?"

"No." Miranda shook her head. "But my contact is. She's with the team in charge of moving Oriana and her family. She should be in one of the private rooms. Come on." She said, leading him into one of the club's side rooms.

Inside, there was a purple-skinned Asari, waiting for them. "Ms. Lawson, I'm glad you made it." The Asari said, pushing herself from her leaning position on the wall. "There's been a complication."

"What happened?" Miranda asked, getting worried pretty much instantly. "Is everything alright?"

"She's fine. But you listed a man named... Niket as your trusted source? He warned that your father has sent Eclipse mercenaries to make a sweep." She explained. "He suggested that the mercs might be watching for you personally. He suggested he escort Oriana's family to the terminal instead."

"Can we trust this Niket person?" The Doctor asked of Miranda.

"With our lives." Miranda answered instantly. "He's a friend. He and I go back a long way..."

"Do you want to bring in any of your other contacts, Ms. Lawson?" The Asari inquired.

"No. You and Niket are the only two I trust on this."

"What about the Eclipse?" The Doctor wondered. "Shepard and I were able to make it through their base safely, but that was relatively undefended."

"I knew I should've brought along some of the other crew, but I wasn't expecting this to happen."

"That's Murphy's Law for you. 'What can go wrong, will go wrong.'" The Doctor remembered the age-old saying. "But I might be able to call in some help, if you'd like."

Miranda thought about it for a moment. "Do it."

The Doctor nodded, and stepped out of the small room. He walked over to the TARDIS, pulled the phone door open, pulled the phone of the hook, and dialed 07700 900461. The phone rang, and a moment later, it was picked up.

 _"Hello?"_ The voice of the metacrisis Doctor greeted him.

"Listen, could you put Jack on?"

 _"Hold on-"_

 _"Yello?"_

"Jack, listen, I need your help."

 _"Reeealy?"_

"Okay, let me put it this way. I don't need your help, a beautiful woman needs your help."

 _"...I'm on my way."_ Jack said, before the call cut. Seconds later, lightning erupted next to the TARDIS, and Jack appeared, clad in his signature WWII coat. "Now, where's this beautiful woman that needs me?"

As soon as Jack asked that, Miranda left the room and approached the Doctor. "Is he the one who's supposed to be helping us?"

"Yep! It was either him, or River. And I'm not too sure how to get in contact with her right now."

"Hello, gorgeous." Jack smiled, holding out his hand. "Captain Jack Harkness."

"You still have a wife." The Doctor reminded him.

Jack instantly pulled his hand back. "Sorry about that, when I see a beautiful person, I just can't help myself. So, you need my help?"

"I'll fill you in on the way." Miranda responded. "Come on, I've arranged for a car to take us where we need to go." She guided the two men out of the bar, and led them to a skycar depot on the edge of the spaceport. The three got into one of the cars, and rocketed off, heading to their destination.

* * *

"Wait, so our plan is to act as a diversion?" Jack repeated, as the car flew through the skylanes of Ilium.

"That's correct." Miranda responded, piloting the car along. Then, engines whirred loudly as two aircraft came up on both sides of the car.

"Gunships." The Doctor said the word with a bad taste in his mouth. "Three guesses where they're going."

"Same place we are." Miranda stated, following the gunships. She put the skycar into a dive,and the Eclipse mercs started shooting at it. A moment later, the gunfire stopped, but the car hit the ground unceremoniously, and slid to a rough stop.

"Another happy landing." Jack smiled, easing the mood.

"Let me do the talking." The Doctor said, as the door opened and they all got out. "I'm good at talking. Hello!" He waved, as they (for some reason) walked closer to the vicious people with guns. "I understand you work for a man named Henry Lawson?"

"What's it to you?" The lead merc crossed his arms.

"You see, he's trying to kidnap my friend's sister. And I really don't like that. Or kidnappers, in general. So, why don't you call off this operation of yours, before we're forced to do something we'll all regret?"

"You think you've got it all figured out, do ya?" The merc Captain chuckled humorlessly. "This is a lot more complicated than you think."

"Not really. Miranda here rescued a child from what was going to be nothing more than a lifetime of pain, misery, and abuse. And you're trying to force her into that life. I don't blame you, really, you're just hired guns. You do what you're told. So, I'm going to give you this one chance: Leave the girl alone, let us leave, and we'll put this all behind us."

"And if we don't?"

"Then you'll have to deal with me." The Doctor threatened, his voice low, almost dangerously so.

The merc Captain's eyes narrowed, and the Doctor held his stare. The merc sighed, and began speaking. "I can't do much about the girl. Captain Enyala's in charge of this operation, so if you want this to stop, you'll have to go to her. I'll do what I can to keep my men from firing on you, though."

The Doctor smiled, and patted the man on the back. "See, now was that so hard? Don't worry, me and my associates will be out of here in a jiffy." He motioned for Miranda and Jack to catch up to him, and the three broke into a sprint, intent on getting away as fast as possible. "Oh, and look into getting out of the whole mercenary business!" He shouted, as they disappeared into the distance.

* * *

"How did you do that!?" Miranda asked, as they ran through the cargo loading bay.

"Practice." The Doctor answered as they turned a corner. "Besides, he seemed like a reasonable fellow. You just need to know the right buttons to push. Ah, a lift!" He fiddled with the control panel, causing the door to open, allowing them access. "Right... any idea which floor they're on?"

"We're going to have to cut through the cargo processing yard." Miranda answered.

"Cargo Processing Yard it is..." The Doctor mumbled, pressing the elevator controls. The elevator car gently shuddered as it moved up the shaft. Eventually, the elevator stopped, and the three stepped out.

As soon as they spotted the three, the Eclipse in the large space opened fire, sending the three to dive into cover.

Miranda, along with Jack, opened fire on the Eclipse. She spotted an explosive canister, and shot it, sending the Eclipse close to it flying. The Eclipse that weren't close to the canister when it exploded were then tore into by the gunfire.

 _"This is Enyala."_ One of the radios on the dead mercs chirped. _"Keep the bitch back! Niket is nearing the transport terminal!"_

"Come on!" Jack ushered. "I'll patch us in to their comm channel, but we've got to keep moving if we want to get to your sister first."

Miranda nodded, and led the Time Agent and the Time Lord through an open cargo container, deeper into the processing yard.

"Mechs!" Jack shouted.

"I've got them!" The Doctor responded, popping out of cover to aim the sonic screwdriver at the automatons. He pressed the activator, and the mechs exploded.

 _"I don't care how many mechs we lose, just stall them damn it!"_ The radio chirped again, the same voice as before behind it.

Then, gunfire started up again, and they scrambled into cover.

"They're on the other side of that gap!" The Doctor reported.

Miranda peeked her head out to see for herself, and spotted some more explosive canisters. All it took was a single shot for one of them to explode, and cause a chain reaction, which set every merc within the blast radius ablaze.

"You'd think they'd have higher standards for storing fuel tanks." Jack commented, looking at the blazing inferno.

"At least it wasn't Peragian fuel." Miranda remarked. "Come on, it looks like we're clear."

"They aren't putting up much of a fight." The Doctor stated, as he followed Miranda and Jack out of cover.

"I think these Eclipse are just cannon fodder. Meant to stall us." The Cerberus operative hypothesized.

 _"Divert everyone except my guard."_ Enyala ordered the listening Eclipse. _"I'll handle Niket and the girl myself."_

"We have to keep moving!" Miranda ordered, breaking out into a sprint. Jack and the Doctor followed, and they fought through the cargo yard.

The yard was a sprawling complex of twists and turns, and it was filled with Eclipse at every corner. The mercs couldn't do much against the three, however. Between the Time Lord, the Time Agent, and the Cerberus Operative, the mercs had their work cut out for them.

The three plowed through the Eclipse, using their surroundings to their advantage. At one point, Jack even managed to use his sonic blaster to make a crate fall on a bunch of unsuspecting Eclipse troopers.

Eventually, the three made it to an elevator at the other end of the facility.

 _"Niket has reached the terminal._ " Enyala reported to the other Eclipse members. " _He'll switch the family over to our transport._ "

Miranda froze in her tracks. "Niket? But..."

"Who is this Niket?" Jack inquired, as they all stepped into the elevator.

The Doctor hit the button, and the elevator shot up the shaft.

"When I was growing up, Niket was the only person who I considered a friend." Miranda answered. "He helped me escape from my father when I finally decided to leave. He knows about Oriana, but he'd never... Maybe Enyala knows we're listening in and she's feeding us misinformation?" She suggested, desperately clinging to the hope that her oldest friend hadn't betrayed her. "Damn it, why can't this thing go any faster!?" She slammed her hand on the controls

"Sorry, but this thing," Jack held up the vortex manipulator, "is designed to listen in on all sorts of frequencies without being detected. They've got no idea."

"But Niket- He wouldn't-"

"Betray everything you stood for?" The Doctor finished, crossing his arms. "Miranda, is it possible that maybe you just don't know him as well as you thought?"

"Niket's the closest- no, the _only_ true friend I've ever had. I know him better than anyone, he wouldn't just betray me like this!"

The Doctor placed his hands on his chin. "Does he know about how you took Oriana with you?"

"Not until recently. I would've just done the same as we'd always had when moving her and her family. But this time, it was just... too personal to involve anyone else. But he knows what I've been through, he'd understand why I did it!"

"Maybe." The Doctor conceded. "But money is a pretty powerful motivator for people. If your father got to Niket, made him an offer he couldn't refuse..."

"He wouldn't betray me like that." Miranda shook her head. "We'll be at the transport terminal soon, and we'll clear all this up."

But unbeknownst to her, Murphy's Law would rear its ugly head once again.

* * *

"...Listen to me, I've got authorization to change their booking!" A man in civilian garb, presumably Niket, said to an Asari transport officer.

"I'm sorry, sir, but we're under security lockdown." The officer said. "Until it's lifted, passengers can not be rebooked.

"This isn't worth my time, Niket." Another Asari, this one in Eclipse armor (and presumably Enyala), told the man. "I get paid no matter how the girl gets to him."

"No! I was told that I could handle this my way. We're not traumatizing the family any more than we-"

"Ah, hello!" The Doctor said, deciding to make the group's presence known. "Sorry we're late, but you know how it is."

Niket's eyes gran over the group, before stopping on Miranda. They widened once he realized who she was. "Miri."

"This should be fun." Enyala hopped off the crate she sat on, and readied her gun. In response, Jack and Miranda did the same.

The Asari transport officer, meanwhile, moved to run from the conflict that was sure to ensue, and was gunned down by Enyala for it.

The Doctor glared at the Eclipse captain. "Big mistake."

Enyala laughed. "What?"

"You just killed a defenseless woman in cold blood. That is _not_ a good place to stand with me." The Time Lord stated, voice steely.

"Niket." Miranda began, steering the conversation away from where it was currently headed. "You sold me out. Why? You were my friend, you helped me get away from my father."

"Yes! Because you wanted to leave. That was your choice. But it I'd known you'd stolen a baby-"

"I didn't steal her! I rescued her!"

"Rescued? From a life of wealth and happiness? You weren't saving her, you were getting back at your father."

"Wealth and happiness? You know as well as I do that the same things that happened to me would've happened to her!"

"I can't believe this!" The Doctor yelled. "You're in a fuss about Miranda kidnapping Oriana, and now you're going and doing it yourself!"

"We're not kidnapping her. We're rescuing her." Enyala turned those words back on Miranda. "Come on, Niket. Let's finish this bitch off and get out of here."

"Take your best shot." Miranda sneered.

"I was just waiting for you to finish getting dressed. Or does Cerberus really let you whore around in that outfit?"

"Everybody calm down!" Jack ordered. "Miranda, if he's been sent by your father, then he knows about her family. You can't just keep moving her and hope for the best."

Niket bowed his head. "Miranda's father has no information about Oriana and her family. I knew you had spy programs in your father's systems, so I didn't say anything. I'm the only one who knows."

"Which means that your the only loose end. This isn't how I wanted it to end, Niket. I'll miss you..."

"Miranda Lawson, you drop that line of thought right this second."

"Doctor, you don't understand. It won't end here. My father will keep trying to find Oriana."

"Well, maybe Mister Niket here can help us. Right?"

"I-I'll tell him you hid her." Niket stammered. "That I don't know where she is."

"Fine. Just... Get out of here." Miranda ordered. "I never want to see you again-"

A loud gunshot then rang throughout the warehouse, and Niket dropped to the floor, dead.

"Done." Enyala said. "Now if you'll excuse me, I've got a package to deliver."

Miranda's biotics flared, and Enyala was pulled into the air, in stasis. "You'll die for that, bitch!" Miranda then threw the Asari clear across the room.

Then, all hell broke loose. More Eclipse started rushing in, firing their weapons.

The three fought as hard as they could, as biotic energy and weapons fire flew through the air. A bolt from Jack's sonic blaster hit Enyala, and tore clean through her barrier. Then, a warp from Miranda shredded the Asari's armor. After that, gunfire from the two did the rest, and killed the Asari. After that, there was only the last little Eclipse to deal with, and they were all promptly taken out as well.

With the room clear, the three entered the elevator, and set it into motion.

"I can't believe Niket sold me out." Miranda shook her head. "I didn't even see it coming..."

"Even with all that genetic engineering, you're still just human." The Doctor stated.

"But I let it get personal, and... I screwed up."

"Miranda, we all make mistakes." The Doctor comforted. "But don't wallow in your own self-pity because of them. Learn from them, use them to make yourself a better person. It's not going to help instantly, but I guarantee you this: You _will_ feel better." The elevator stopped, and the door slid open. "Now come on, let's go see Oriana off."

They all stepped out, and walked into the transport depot. "No sign of Eclipse." Miranda said, looking around. "It looks like we're in the clear." Miranda stopped looking around, and turned her attention to the small family waiting to board the transport. "There she is." Miranda smiled, looking at the youngest woman, who was the splitting image of Miranda. "She's safe... with her family." For a moment, Miranda looked sad, and maybe just a tad bit regretful. "Come on, we should go." She said, putting on the mask once more.

"No." The Doctor shook his head. "We're not finished."

"What do you mean?"

"You're going to go introduce yourself. Let her know that she has a sister that cares for her, and won't ever, ever stop."

"Doctor-"

"Miranda, is it really so bad for her to know that she has a sister who loves her?"

"I guess not..." Miranda conceded. She swallowed her pride, and walked over to Oriana. The two talked for a few moments, and Miranda walked back over to the Doctor and Jack, smiling the biggest smile the Doctor had ever seen her have. "Come on." They all walked into the elevator, and Oriana smiled one last time at Miranda, and the door shut, the elevator taking them to their destination.

* * *

"I think that went pretty well, don't you?" The Doctor asked, as he and Miranda strolled into the TARDIS, Jack having gone back to the Doctor he knew.

"Yes... I suppose it did." Miranda returned.

"Now then, we should be getting back to the Normandy. Susan!" The Doctor called. "Is she fixed yet?"

"Yep!" Susan confirmed, walking up the stairs, holding a tub of ice cream.

"Excellent!" The Doctor hopped around the console, and pressed the fast-return switch again, and the TARDIS dematerialized into the Vortex. Seconds later, the engines slowed to a halt, and the TT capsule landed. "Here we are! Miss Lawson, you should get back to your station. Before Shepard realizes you were gone."

"I'll do that." Miranda nodded. The Doctor escorted her to the door, but before he could open it, Miranda pulled him into a hug.

"...eh?" Was all that the Doctor could say, being as confused as he was.

"Thank you." Miranda said, before releasing him. "Now, I should return to my post. Be seeing you." She walked out, and the door shut, leaving the Doctor and Susan alone in the console room.

"Grandfather, what just happened?" Susan asked, not believing her eyes.

The Doctor however, just smiled. "Oh, it's very simple. The Ice Queen's just started defrosting."


	25. Regeneration

_The TARDIS Library..._

Susan sat waiting in one of the chairs on the second level of the TARDIS's massive library. For some reason, the Doctor told her to wait there for him. Curious, Susan obliged.

Susan waited for about five minutes, before her grandfather entered, clad in the ornate robes many Time Lords also wore. "Grandfather?"

The Doctor cleared his throat, and started speaking, with an unusually formal tone. "Arkyitor of Lungbarrow House, the time has come for you to be administered the Final Test. I trust you've been keeping caught up with your studies?"

"Of course, Grandfather."

"Then let's not delay." The Doctor said, walking over to a storage compartment on the wall. The compartment's door was usually locked, but this time, it slid open effortlessly, allowing the Doctor to pull out a large book(well, more of a tome, really). He opened the book, and started reading from it. "Being a Time Lord is no small task. It falls to us to uphold the Laws of Time, and serve as guardians of the timeline, do you understand?"

"Yes."

"Then you will answer every question this presents to you." The Doctor said, putting the book down in front of Susan. "You must answer to the best of your ability. Understood?"

"Yes."

"Then you may begin." The Doctor responded, moving to exit the library. He walked through the maze-like corridors of the TARDIS, and back into the console room. He tuned one of the monitors to show a live security feed of the library, and began to observe as Susan took her test.

Susan was doing quite well, in all honesty. Most of the questions on the test were designed to confuse and deceive, to weed out the students that were sure to become renegades, from those that would likely be model Time Lords. The rest of the questions were design to test the knowledge of temporal mechanics, and the Laws of Time.

It was a few hours later when Susan sighed in relief, and closed the book. The book then disappeared as it was reclaimed by the TARDIS, and Susan's test results were displayed for the Doctor.

After reading over the results from the test, a grin split the Doctor's face. He pulled a small box out of a secret compartment in the floor, and ran off to the library.

"Susan," The Doctor began, approaching the young Gallifreyan, "Congratulations. You just made Time Lord."

"Yes!" Susan excitedly shouted.

"Now, considering that we can't get you a TARDIS, I've settled for this." The Doctor said, holding out the box, with Susan's name transcribed on the top. "Think of it as a congratulatory present."

Susan slid the top of the box off, and looked in. "It's a Sonic Screwdriver..." Susan commented. She reached in, and pulled the device out. It was a tiny thing, practically dwarfed by the Screwdriver the Doctor owned. Its casing was taken from one of the spare screwdrivers the Tenth Doctor had abandoned, and it had a black grip, as well as a green emitter.

"Yup!" The Doctor said. "Not a very original design, mind you, but the TARDIS was itching to get rid of some of the spare parts in the storerooms. Now then, what do you say to a trip? Take the new Sonic out for a test drive, so to speak?"

"Can we go to the future this time, Grandfather?" Susan asked, as they walked through the corridors of the TARDIS.

"I don't see why not." The Doctor said, walking up to the console. "The real question is- Oh, hello..." He said, as something on the console started beeping. Almost as soon as it did, the engines engaged, and the TARDIS took off of her own free will.

"Grandfather, what's happening!?" Susan asked holding onto the railings.

"Apparently, the TARDIS thinks we're supposed to be somewhere." The Doctor stated, looking at one of the console readouts. "I don't think I like where this is going..."

"Grandfather...?"

"Right -er- how do they say it? Ah, yes, I've got it. Brace for impact!" As soon as the Doctor said that, the TARDIS's engines gave a loud thud, and they were thrown to the floor. "Ohh, that's going to hurt tomorrow." The Doctor groaned, as he got up. "Susan?"

"I'm okay, Grandfather." Susan responded. "Any idea where we've landed?"

"I don't know... let's find out!" He said, rushing over to the door. He popped his head out, and stepped out slowly. "This looks like the Citadel Archives, but I don't recognize the area..."

"Wait, you've been here before?" Susan asked.

"Hmm? Oh, yeah. I decided to go on a little TARDIS trip while you and the rest of the Normandy crew were sleeping. Wanted to see if they had any more data on the Reapers. Origins, a weakness, things like that."

"Okay, I suppose that narrows it down. But when are we?"

In response, the Doctor stuck a finger in his mouth, pulled it out, and held it in the air. His eyebrows raised slightly. "Twenty-one-eighty-six. Not too far ahead than when we left. Only about six months."

"Well, at least I get to go to the future."

"That's the spirit! But why would the TARDIS bring us here, of all places?" The Doctor wondered. Then, his head turned as he heard something. "You hear that? It sounds like Shepard. Come on, but be quiet." The Doctor said, as he and Susan sneaked through the hallway. As they closed in on one of the vaults, they could hear talking.

"...short answer is no. They're not." Shepard said, to somebody else. A few shots echoed throughout the room, but all in all, everything seemed calm. "The long answer involves your friends being trapped in iridium vaults and being forgotten for... well, forever."

"Others know about this, about you." _Shepard_ said in response, causing Susan and the Doctor to look at each other in confusion. "The Alliance will stop you."

"What do you think, Staff Analyst Brooks? Will the Alliance stop us?"

"I wouldn't know." Another woman said. It seemed the conversation was about to take a turn for... Well, the Doctor didn't actually know. "I don't actually work for them."

The mood was getting tense, but nevertheless, the Doctor poked his head around the corner. "Oh..." He breathed, looking at the scene in front of him.

There were two Shepards. One, in strange armor, standing in front of a blue force field. The other, in the correct armor, tapped behind that field. As far as the Doctor could tell, there weren't any time-traveling shenanigans (beyond his own) going on, which meant that the other Shepard... was a clone.

"What was the point of it all?" Proper Shepard inquired, anger making itself apparent in her voice.

"All we really wanted was your Spectre code." Brooks answered. "But then you survived the hit, and insisted on bringing your damned Asari into it. So I had to tie up loose ends."

"The arms dealer..." Shepard said, seemingly realizing something.

"But then your sex bot," _'Sex bot?'_ "just had to go and recover the data. So here we are. Forced to... contain the situation."

"Who the hell are you anyway?" Shepard asked. "And what makes you think I won't track you down?"

"My name doesn't matter." 'Brooks' answered. "I don't keep the same one for more than a few days. And if the Illusive Man hasn't found me yet, well... You never will."

"You're Cerberus?" Rage was now slowly creeping back into Shepard's voice.

"Was." Brooks answered. "Mr Illusive and I didn't see eye to eye. He's indoctrinated, whereas I prefer the whispers in my head to be my own."

"Well then why not come to me? We could've worked together."

"We did. In a way. I was the one who put together all those dossiers on your 'Suicide Mission.'"

"The Collector Base?"

"There was the Salarian Doctor, the Asari Justicar, the Quarian... Nice to have finally met you, Tali."

"Charmed." Tali sarcastically replied.

"They were all mistakes. We were a pro-human group who started looking to aliens for help. So I bided my time, and when I found another you who agreed..." Oh, how little this Brooks and the Clone knew. "...I woke her up."

"Fair warning; no one who's ever betrayed us had ever survived." Shepard threatened.

"And yet they keep trying." A krogan (Wrex, if the Doctor remembered from his reading up on the original Normandy correctly) to the left of Shepard added.

"You two may think you're clever. And yeah, you were-just a bit-but clever can't beat a bullet. And yeah, maybe I'm trapped in here, but _don't_ get comfortable. Because that bull's-eye on your back is getting bigger by the second." Shepard spat.

"That sounds very dramatic. And if someone like, say, Commander Shepard made the threat, I'd be worried." Brooks condescended. "But you're _not_ Commander Shepard. Not anymore."

"You had Miranda, I have her." The Clone said. "Mine has more bite."

"It was fun while it lasted." Brooks said, with a mock-sad tone of voice., as the Clone walked over to a computer terminal.

"What are you doing?" Shepard demanded.

"Setting things right." The Clone responded. "Remember this?"

"You are the first human Spectre, Commander." A holorecording of the Asari Councilor said. "This is a tremendous accomplishment for you, and your entire species."

"Except somewhere along the way, you forgot about your species." The Clone spat as the recording disappeared. "You've saved more alien lives than you have human."

"All species matter, not just humans." Shepard retorted. Then, she fired off a rueful smile. "Besides, I'm sure you'll be thinking that way once you find out what's _really_ going on inside you."

The Clone just gave a humorless chuckle. "You know what they can't duplicate? Our handprint. Life gives it its shape, not DNA... which is a problem. Computer:" The Clone prompted. "Update Council records. Subject: Shepard, human Spectre."

"Accessing record." The Computer responded. "Please input new data." The Clone placed her hand on the Computer's scanners. "Biometric identification updated. Good day, Commander Shepard."

The Clone and Brooks then began walking away from Shepard's team. "Now if you'll excuse me, the Normandy needs its captain. So..." She turned to the real Shepard. "I should go."

"Farewell, Commander." Brooks sneered. "I guess this is where 'legends' go to die." She said, leaving the room, as the vault slid shut, sealing the real Shepard and her crew inside.

The Clone and Brooks, meanwhile, walked straight past the TARDIS, paying it no attention, and not noticing the Doctor and Susan. Once they had left, the Doctor and Susan popped out from their hiding spot, and walked into the room the other two had previously been in. The Doctor walked over to the control panel, and opened the vault back up.

"Doctor? How did you get here?" Shepard asked,

"TARDIS, of course, but that's not important right now."

"Right, evil clone." Shepard nodded. "Come on, we can use the TARDIS to get ahead of them."

The Doctor nodded, and they all stepped into the timeship. "Right, sorry, I'm still very lost. Since when do you have an evil clone?"

"Apparently they grew her for spare parts." Shepard remembered. "When Cerberus brought me back, they weren't entirely sure how many of my organs were still salvageable. Turns out they didn't need her, though."

"Ah. Right, I'm assuming the big hole outside was made by you guys?"

"That's right."

The Doctor simply nodded, and set the TARDIS into motion. Seconds later, it rematerialized, and they all stepped out.

"What?" Wrex said, looking over Shepard's squad, who were most definitely not outside last they checked. "How'd you all get ahead of us?"

"Oh..." The Doctor's face fell once he had realized what happened. "I knew I was forgetting to check the helmic regulator when we were doing maintenance the other day."

"Well, not much we can do about it now." Shepard said. "What have you all been doing."

"We're waiting for Joker." Garrus answered. He looked to the artificial sky to see a skycar take a dive, and come in for a landing. "There he is."

"I've got room for Shepard plus two." Joker stated once the car landed. "And make it snappy because the other Shepard is stealing my ship!"

"No need for that. Quick, everyone, into the TARDIS!" Shepard ordered, and she ushered her squad in (including Joker, who seemed to be moving oddly fast for someone with glass bones syndrome), to the Doctor's protest.

"Hold on!" The Doctor shouted. "The Helmic Regu-"

"Look, do you want the Normandy to be stolen or not!?" Joker snapped.

"Er, well, no."

"Then shut up, and get us to bay D-24!"

"Right, D-24." The Doctor mumbled. "It's not like you all just barged your way in, and made yourselves at home. Susan! Hold that lever down. Without the Helmic working properly, that's the next best thing we have." He ordered, setting the TARDIS into motion. Again. "So, why don't you all fill me in really quick, eh?"

"Well, after you, River, and Susan went on your own little vacation, I got a message on my private terminal in my apartment."

"You own an apartment?"

"Anderson gave it to me." Shepard shrugged. "Anyway, the message was from Joker, or I thought it was, at least. So I go to the sushi place that was mentioned in the message, and Joker tells me that I invited him, not the other way around. So then Brooks runs up, tells me someone's trying to kill me, and then we all get ambushed by mercs. Long story short, we made it back to safety, and get a lead to a casino owner who can trace the gun. The owner was dead, but we managed to figure out that we needed to go to the archives. Then, we met the clone, she filled us in, and we fought our way through only to be trapped in a vault at the end of it."

The Doctor sighed "Why can't anything ever be-" A blinking light on the console caught his attention. He looked at one of the console monitors, and said: "Uh oh. It looks like the fake Shepard's already sent out the departure request."

Shepard turned to Joker. "Can you try to get Citadel Control to deny it?"

"Tried" Joker shook his head. "All the comm lines in the area are jammed... probably to make it easier for them to steal my ship!"

"We'll stop them." Shepard vowed.

"Shepard!" A woman with EDI's voice began, sounding alarmed. "You clone has entered the ship, and is attempting to-" Her body began beeping and whirring wildly, and the holographic visor around her eye shut down, as EDI slumped over, seemingly sleeping.

"EDI?" Liara looked the gynoid shell over.

"Is she supposed to do that?" Wrex asked.

"Well... this is awkward." Tali stepped back from EDI's shell body.

EDI's eyes snapped open, and she looked back up, standing upright. "I'm okay!" She proclaimed, even as her eyes were looking around in different directions. She straightened her eyes out, and smiled.

"Really?" Joker deadpanned.

"The clone has disabled my control of the Normandy, as well as all sensory input." EDI reported. "I cannot lock her out, or counteract her commands."

"Are you still in fighting shape?"

"I am experiencing a significant feedback loop in my head, and an increased desire to kill your clone."

"Get in line."

"Right, here we are!" The Doctor said. "The Norm-"

The TARDIS seemed to collide against something, and the console sparked as the console room violently shook, while the engines struggled to maintain flight. The Doctor pulled the emergency-stop lever, and the TARDIS calmed. "What the hell was that!?" The Doctor yelled, as he righted himself.

"Oh... that's probably the anti-TARDIS shield." Garrus admitted. "The Clone must have turned it on."

"Anti-TARDIS!? Why would you have an- you know what, never mind. I'm sure I'll find it out eventually."

"Come on, you guys!" Shepard ordered, throwing the TARDIS door open. "Well, at least we're on the Normandy." Shepard said, looking around the airlock.

"Wait, what!?" One of the Normandy's crewmembers (who was in the process of leaving the ship) asked, turning around. "You were just _on_ the Normandy. You... you fired me! Dishonorable discharge for conduct unbecoming! You kicked me off the ship with barely enough time to grab my toothbrush."

"Traynor," Shepard sighed, "I can't just _fire_ you. I need to give a disciplinary hearing first. And really, the first thing you grabbed was your toothbrush?"

"It's a-"

"Ciscion ProMark 4." Shepard interrupted. "It uses tiny mass effect fields." She droned. "I know that because I'm the real Shepard."

"Wait... If that wasn't you, then-"

"Evil Clone, sort of a long story." Garrus said, as he and Liara worked on getting the inner airlock door opened. The door control flashed an angry red, and then vanished. "Damn. Locked tight."

Shepard turned to Traynor. "Is there anyone still on board that can help us?"

"No." Traynor shook her head. "I was only here because I was part of the retrofits back on Earth. Everyone else is on shore leave."

"Then you're the only one who knows of a way inside the ship." Shepard assumed. "Can you get me inside?"

Traynor walked over to the middle of the airlock, and started looking for something on the floor. "There's an emergency exit hatch for evacuations. It should be right... here!" Traynor pulled up one of the floor grates, revealing a metal trapdoor set into the floor.

Shepard started to look for a way to open the hatch, but there was nothing. "Manual lock, and it's only meant to be opened from the other side. Any ideas?"

"Oh, I've got it!" The Doctor said, reaching into his robes. His face fell once he realized he was still wearing them. "Oh.. I must've left it in my other jacket. I knew it was a bad idea to wear this thing."

"Yeah, I wasn't going to comment on it." Shepard snarked. "But any day now."

"Susan." The Doctor turned to his granddaughter. "You're up." He pointed to the hatch."

Susan nodded, crouched down to get closer to the hatch, and pulled out her own sonic screwdriver. She pressed down the activator, it buzzed, and she ran it along the line where the two small doors met. The hatch's locking mechanisms clicked, and the hatch opened up.

"Good job!" The Doctor patted Susan on the back.

"Okay, Traynor, you're probably going to want to go ahead and get out of here." Shepard suggested.

"Right, good idea." Traynor nodded. "Oh, and good luck." She wished, before running from the airlock.

"Alright, everyone in, one at a time." Shepard ordered, taking point and hopping into the small crawlspace. "Doctor, you and Susan stay at the back."

The Doctor nodded, and he and Susan stayed back while the others hopped down first. Once they were sure to be the last ones, they hopped down, and the hatch sealed behind them.

As they crawled along, one of Shepard's crew sneezed.

"Vega!" Shepard whisper-shouted.

"Sorry." The marine whispered back. "It's dusty as shit in here."

"You'd never find this much dust on a Quarian ship." Tali remarked.

"Shh!" Shepard ordered, as they came to the end of the tunnel.

"...Hey, what'd she mean 'slow her down?' We're allowed to kill Shepard if we have to, right?" One of the mercs said, conversing with his partner.

"She said 'slow her down' because she thinks we're cannon fodder." The other merc responded.

"Oh. Well... shit."

It was at that moment, Shepard took the opportunity presented to her. She hit a button, and the hatch (really just the stairs used to step up into the corridor leading to the bridge) flipped up, and they all started firing.

"Watch it!" Shepard yelled, as she and the team spread out, firing on the mercs. "I don't want to be fixing the bullet holes when we're done!"

"Fuck it, the maintenance crews will have to do it anyway!" Vega shouted.

"Good point, fuck it!"

"Oh yeah, one of my favorite places to fight!" Garrus shouted in earnest, as he put a bulled right through a small hole in the large shield a merc was using, and through the merc's head.

"The CIC of a warship?" Tali asked in response, setting loose her combat drone on the mercs.

"Right there above the gardens, and below the electronics shops!"

"And antique shops, as I recall!" Shepard butted in.

"But only if they're classy!" Garrus responded.

The team members with guns quickly took care of the intruding mercenaries, and the CIC calmed, though it was still full of spent thermal clips and dead bodies.

"Right, that's the last of them." Kaidan stated, after doing one last sweep of the room.

Shepard simply nodded her acknowledgement. "Then let's go finish this. Kaidan, James, you two stay behind and take care of the pilot." She ordered, stepping into the elevator. She looked at the controls, and pressed the button to take them to the shuttle bay. The elevator shuddered, and it set into motion, proceeding down the small shaft that it occupied.

The elevator hit the bottom of the shaft, and stopped. The doors opened, opening up into the shuttle bay. Various crates were haphazardly stacked on top of each other, and tools from the repairs were left scattered in various places.

The team stepped out of the elevator, and spread out, looking left and right for any sign of the Clone. They didn't need to look for long, though.

The Clone stepped out from behind a stack of crates, wearing a set of Shepard's N7 armor, only this one was repainted silver and blue, as opposed to the black and red Shepard wore.

"Well, that's creepy." The Commander remarked, as she turned her weapon on the duplicate.

The Clone immediately started firing, and ducked into cover. Shepard promptly returned fire, and ducked into cover herself.

"You want to stop shooting up my ship?" The Clone yelled.

"It's not your ship!" Shepard responded, with all the fury she could take making its way into her voice.

The Clone laughed, an especially eerie sound. "It will be. I've taken your name, your Spectre rank, even your fingerprints!"

"And what're those going to get you when you're dead, huh? It's seven against one, here! Face it; you've lost!" Shepard retorted.

The Clone just laughed again. "You're underestimating my strength. You see, I've got something you don't."

"And what is that?"

"This." The Clone popped out of cover, and glowed blue with biotic energy. The energy surrounded her like a ball, and she charged forward like a gunshot, on a course to collide with Shepard herself. The Clone hit the Commander, throwing her to the ground. The Clone then moved away from the squad, firing on them as she did so.

 _"Commander, we got problems up here!"_ Kaidan reported, radioing in.

"What now!?" Shepard yelled, as she got back up. She proceeded to fire at the Clone, but damn, that bitch was tough.

 _"We tried making it into the cockpit, but the pilot sealed himself inside."_

"Look, I don't care if you have to blow that door open! Just get inside and stop him!" Shepard yelled, dodging more gunfire.

 _"Commander, this is Cortez."_

"Shit, I knew we were forgetting someone back at the archives."

 _"Don't sweat it, ma'am. Listen, I'm going to try and keep the Normandy from going into FTL. I'll do what I can, but I don't think I'll be able to do it forever."_

"So, finish what I'm doing down here, fast. Got it." Shepard responded. Then, the deck beneath her shook, and became unsteady as the Normandy leaned from left to right.

"What the hell's going on up there!?" The Clone barked into her comm. "Get us into the nebula and into FTL!"

 _"We can't, a skycar keeps blocking our path!"_ The merc pilot responded.

"Then shoot it!" The Clone ordered.

The sound of the Normandy's main cannon firing filled the shuttle bay, as the shots caused the ship to shake ever-so-slightly.

"Damn it!" The Clone cursed, after she noticed that every attempt to shoot down Cortez had failed. "Launch the shuttle, and blow that thing out of the sky!"

In response, the door of the shuttle bay opened up, and the shuttle shot out, chasing after Cortez's skycar.

But that did nothing to stop the fighting in the shuttle bay. The gunfire continued to ring out, and bullets scattered, as biotic blasts flew through the air.

"Susan, I think that it may have been a good idea for us to just stay in the TARDIS." The Doctor told his granddaughter, as they hid behind cover.

"You think!?"

"She's out of medigel!" Shepard yelled.

The Clone still had the layers of armor protecting her, but that didn't stop Shepard from landing a hit that kicked the gun out of the Clone's hands. The Clone retaliated, and performed a biotic pull that pulled the gun out of Shepard's hands.

Now, the two could only fight with their fists. Shepard broke into a sprint, and charged at the Clone, tackling her to the floor, and causing them both to roll down the shuttlebay ramp. The two stopped rolling, and the real Shepard came out on top, pummeling the Clone with all her might.

The Clone channeled the last bit of strength that she had, and pushed Shepard off. The Clone then began to right herself, but the Normandy swayed again, and both Shepards slipped off the ramp. The Clone and the proper Shepard grabbed onto the edge of the ramp, and hung on for dear life.

"Look at you." The Clone grunted, as she tried to pull herself up. But there was nothing to grab onto, only the smooth metal of the ramp. "What makes you so damned special? Why you, and not me?"

"Shepard!" Tali yelled, running down the ramp, and grabbing onto the Commander's hand.

"We've got you!" Wrex said, as he helped Tali to pull Shepard up.

The Clone, however, had no one. All she did was look at Brooks, a silent plead for help, but all the fake Alliance officer did was turn away, and leave.

"Thanks." Shepard said to her team mates, as she steadied herself. She turned to the Clone, and in that moment, decided what to do with her. "Grab my hand." She ordered, holding her hand out.

"And then?" The Clone responded.

"And then you'll live!" Shepard stressed.

"Why?" The Clone shrugged. She closed her eyes, relaxed her grip, and slipped from the ramp...

Only for someone else to grab her arm.

"I don't think so." The Doctor said, keeping hold of the Clone's arms with both of his hands. "Now, can one of you help me over here? I think my foothold's going."

Shepard grabbed onto the Clone's other arm, and pulled her up, after that, the three got a steady foothold. They all walked back up the ramp, and into the shuttlebay as the situation settled, and everything was as calm as still water.

But at that moment the Clone grabbed a pistol from Shepard's holster, and used it to shoot herself in the heart.

"No!" The Doctor shouted, grabbing the Clone as she fell to the floor. The Doctor shook his head, and gently set the Clone down on the floor.

* * *

"Fortunately, they weren't here long enough to do much real damage." Cortez stated, as he and the others did a sweep of the Normandy's shuttle bay. In the middle of the large room, the Clone lay dead on the floor, with a small tarp covering her body. "Although I may need some help from James cleaning up the mess they made down here."

"Plus they overloaded the head diffusion system firing at him." Joker said, referring to Cortez. "Not sure if you noticed, but shuttle guy over here did some crazy flying to keep himself in one piece.

"It's nice to fly something a bit more maneuverable than the Kodiak." Cortez responded, going back to his station.

"What about EDI?" Shepard inquired. "Is she back online?"

"I am once again in control of the Normandy." The AI informed. "Thank you for asking."

"What about the mercs?" Shepard asked. "Any survivors?"

"Just one crappy-ass pilot and her." Joker pointed to Brooks, who walked into view, in handcuffs. "Alliance is taking her to a high-security facility. Maybe she can give 'em dirt on Cerberus."

"I'll be more than happy to cooperate with the authorities." Brooks snidely smiled.

"Maya," Shepard shook her head, "I know that voice."

"Do you _really_?" Brooks responded.

"You're getting a chance to redeem yourself." Shepard crossed her arms. "Don't waste it."

"So serious. Admit it. Part of you liked having me around, looking up to the legend." She taunted. In response, Shepard shook her head, and turned away. "We had some laughs. And who knows? Maybe we'll have more someday."

"No, we won't." Shepard responded. "Because you are going to stay in your cell and do your time."

"Afraid I'll escape?" Brooks taunted further. "Come back for revenge? Is the great Commander Shepard pleading for her life?"

"I'm pleading for yours." Shepard finished.

"So thoughtful." Brooks sighed. "Well then, I suppose I'm off to lockup... You know, _she_ wouldn't have let me live."

"You can't clone everything." Shepard reflected. With that, Brooks was ushered out of the shuttle bay.

"What about the body?" Garrus asked, looking over at the dead clone.

"...We'll give her a proper burial." Shepard stated, after a moment of thought. "She may have been a total bitch, but everybody deserves one."

The Doctor's eyes widened, as he stared at the clone's dead form. "You know... I think that might not be necessary..."

"What do you mean?" Shepard frowned in confusion.

The Doctor, however, just smiled. "Pull the sheet off her." The Time Lord ordered.

Shepard thought about it for a moment, and then decided to humor him. "Doctor, what are you- What the hell!?" Shepard shouted in surprise, looking down at the clone.

The clone's skin was literally glowing, as golden particles streamed from the clone's skin.

"She's regenerating." The Doctor smiled, looking down. The Doctor then took a step back. "I'd stand back, if I were you." He told Shepard, causing her to take a step back herself.

Then, the light seemed to explode, and more of the golden energy came streaming out of the Clone's skin like fire. The light from the regeneration filled the shuttle bay, illuminating the room like a sun.

After a moment, the Clone's face seemed to morph, the light died down, and the regeneration energy stopped, revealing a different woman in the armor. This woman was ever-so-slightly taller, and had a mass of brown curls on her head.

Everyone who had met this woman before did a double-take.

"River!?" The Doctor and Shepard shouted out in surprise at the same time.

"Oh great, is she stealing other people's faces now?" Tali remarked.

"Shepard," The Doctor began, "I need you to tell me what happened when you met River the second time."

"Well, you brought her back to the Normandy after a trip in the TARDIS, told me she was freshly regenerated, and- ...oh."

"Yeah... 'oh.'"

"So this is the River that I know, just..."

"At the very beginning." The Doctor elaborated. "This is... awkward."

"Considering what was going on just a few minutes ago, yeah." Shepard responded. "So... what are you going to do with her?"

"I'm going to do what time says I do." The Doctor answered. "Besides, she deserves a second chance. The chance to be her own person, not just a clone of Commander Shepard. And this is the perfect way to give it to her." The Doctor crouched down, picked up the sleeping Clone/River, and began carrying her bridal-style. "Come along, Susan." The Doctor told his granddaughter. Susan followed along, and the two stepped into the elevator, taking it back up to the CIC deck.

They then proceeded through the CIC up the stairs, and into the airlock, where the TARDIS was waiting. The Doctor unlocked the doors, pushed them open, and stepped inside.

He gently sat the Clone/River down in one of the chairs in the console room, and set the controls. He pulled the space-time throttle, and the TARDIS dematerialized, taking them back to their proper time.

* * *

 ** _I had originally planned for the River being Shepard's clone 'discovery' to be in the sequel to this story (which will deal with the events in ME3), but then I decided that since I wanted to maintain continuity with Doctor Who, Susan would have to be left behind, so she'd need somebody to keep an eye on her, that someone being River._**

 ** _I could've just done the metacrisis Doctor, but since I wanted River to be a main character in the next one, this chapter seemed like the best course of action._**


	26. The IFF

The TARDIS shook and shuddered as it flew through the Time Vortex, carrying its three passengers gently through the winds of time.

Susan was at the console, trying to keep the TARDIS from jostling around like it usually did, while the Doctor (back in his normal attire) was over by the seat River/the Clone was in, keeping watch over her sleeping form.

River was so... young, unfinished even. The Doctor chuckled at that. It kind of reminded him of what she said when she met his tenth self in the Library.

The Doctor had to pull himself away from that line of thought. That was his River, not the River he was just looking down at. He'd have to be careful not to fall back into old habits when this River finally decided to wake up.

And as if she were responding to that very line of thought, The Clone stirred, and opened her eyes.

"What the hell!?" She yelled, jumping up, and hitting the Doctor in the face.

"Ow!" The Doctor yelled, clutching his nose. "The hitting, is that really necessary!?"

"When you wake up with one of your enemies standing over you, yes." The Clone sarcastically responded. "Now then, where am I?"

"Look, River-"

"Who the hell is River?" She demanded, causing the Doctor to flinch.

"Look, I don't know if you remembered, but you sort of died back there on the Normandy." The Doctor starting, still clutching his nose.

"Sort of?"

"Well, you regenerated. Brought yourself back to life, in a nutshell."

"What are you blathering on about?" The Clone interrupted.

The Doctor held up his hand in the 'hang on a second' gesture, and reached into his pocket. His arm made it elbow deep, and the Doctor rustled around inside the pocket, as The Clone looked on in a mix of befuddlement and confusion. Seconds later, the Doctor pulled his arm back out, along with a small hand mirror.

"Right, you might want to brace yourself for a shock." The Doctor warned, with the mirror's reflective surface turned away from the woman.

"Just get on with it."

The Doctor nodded, and turned the mirror around, allowing The Clone to see her new face.

"What the hell?" She muttered to herself, peering into the mirror. The Clone took her hand, and began feeling her face, watching as her reflection did the same. "That can't be me... It has to be a hologram, or a-"

"River..." The Doctor began, trying to calm her.

"And there you go again!"

"Listen, I understand this is all very confusing for you, but you need to calm down. Deep breaths..." The Doctor ordered, gesturing for her to breathe. After she took a deep breath in, and exhaled, did the Doctor continue. "Now, if you have questions, go ahead and ask them."

"Why did you call me River?" The Clone asked.

The Doctor flinched in response. "Out of all the questions, you had to pick the hardest one..." The Time Lord mumbled, shaking his head. "Hold that thought." The Doctor said aloud, as he moved over to the console. He walked to the panel closest to the door, and pressed a small button. After the button was pressed, a holographic duplicate of the Doctor himself materialized in the nearest vacant space in the console room.

"Voice Interface enabled." The Hologram stated, completely emotionless.

"Go on," The Doctor prompted the interface, "Show us River Song."

In response, the hologram flickered and changed from the Doctor, into the splitting image of River Song.

The clone stepped around her hologram, looking over it up and down. "So... this is... this is me?"

"In a sense." The Doctor answered. Before the Clone could ask what he meant by that, he continued. "Parallel universes and such. That River is the one from my universe."

"Wait... did you say parallel universe?" The Clone asked.

"I just did, pay attention." The Doctor responded. "Technically, you're the alternate version of her. Or she's the alternate of you. Or you're both mirrors of each other. This is why I hate travelling to other universes, it tends to get confusing very quickly."

"So... what am I supposed to do now?" She asked. "Everyone probably thinks I'm dead, considering I shot myself. And to top it off, I'm wearing another person's face! Huh... I didn't used to have a problem with that."

"Well... you could travel with me?" The Doctor suggested smiling warmly.

"Travel?"

"Yep!"

"With you?"

"That _is_ what I just said."

"Travel... where?"

"Everywhere." The Doctor finished, looking at the TARDIS console. "Or anywhen. The TARDIS can take us wherever or whenever we care to go."

For a moment, the Clone was completely silent. Then, she started laughing. "Do you really think I'm just going to take everything you say at face value? You're one of Shepard's friends, I know that. You could be leading me into a trap right now."

"Yes, I could be doing that. But I'm not." The Doctor retorted. "Besides, I can see that look on your face."

"What look?"

"The look that every person has after something terrible's happened to them. You're feeling bad because you've been manipulated by someone you trusted, and the fact that that trust didn't go both ways. And now you want to just be able to get away from it all, if only to have a moment to yourself."

"How are you so sure?" The Clone retorted. "I could just be faking it." She stated.

"I know because I've felt the same way before." The Doctor admitted. "There was a bad day, a long time ago, and afterwards... I just wanted to get away from it all. No more Doctor, no more universe-romping Time Lord, just Theta Sigma, a tired old man who just wanted to be able to sit down and be able to enjoy a minute of calm for a change."

"What happened?" The Clone asked.

"Like I said, it was a bad day. I lost people I cared about. And afterwards, I just wanted it to stop. I figured if I stopped travelling altogether and found an isolated moon to live on, then I'd not have to go through the same thing again."

"It didn't last, did it?" The Clone assumed.

The Doctor smiled faintly. "Yeah. Some things happened. Found myself back on planet Earth during the middle of an invasion by living plastic. Met a girl working in a shop... And after that... Turns out, the universe didn't hate me as much as I thought it did. And I got the closure I needed, in the end."

"Why are you telling me this?" The Clone tilted her head sideways. "I just tried to kill you a few minutes ago."

"I suppose I'm trying to convince you. And to that second one, that wasn't the first time River Song tried to kill me. But the point is, the universe is going to find some way to get you to the place you need to be. Why not take the long way around? And who knows, you might have some fun on the way."

"...What about the people in my own time?" The Clone asked. "Do they think I'm...?"

"They think you're dead." The Doctor finished. "The only people who know you're still alive were with us in the shuttle bay when you regenerated. Beyond them, nobody."

"So I won't be convicted for trying to kill Shepard and trying to steal her ship?"

"Not unless you decide to turn yourself in. At this point in your life, nobody knows who you are. As far as they're concerned, the Clone of Shepard killed herself after being pulled into the Normandy by a madman wearing a strange set of robes."

"Then I have nothing... I'll come with you, I guess." She then shook her head, and silently chuckled. "A few minutes ago, you were trying to help Shepard kill me. But you give me the offer to travel with you, and I have no problem with it!"

"Regeneration." The Doctor simply said. "It tends to have a way of altering personalities ever so slightly. Meaning you'll likely be prone to making decisions differently."

"Okay... Should I have a problem with that?"

"Of course not! It's completely natural!" The Doctor responded. "Now, before we start travelling, you're going to need a name of your own."

The Clone looked at the voice interface hologram, which was still being projected for some reason. "Well, you already said I looked like her, so... why not River Song?"

The Doctor flinched. "Are you sure you have to use that one?"

"It's like you said, we're alternates of each other. Besides, think you can come up with something better?" She asked, eyebrow raised.

"...No." The Doctor grumbled.

"Then River it is." The newly-named River proclaimed. "So, where do we start?"

"First, you do what every freshly-regenerated Time Lord does." The Doctor answered.

"And that is?" River asked.

"A wardrobe change!" The Time Lord responded, pointing to one of the corridors leading out of the Console Room. "Take a right through that door, take the tenth unlocked door on your left, take the elevator up five levels, go straight through the juice bar, then walk for about a mile, and it'll be through the green door. Easy-peasy."

"...Right." River blankly stared, before walking through the door, heading in the completely wrong direction.

The Doctor sighed, and shook his head. "Susan, guide her there, will you?" He said to his granddaughter, who had stayed out of the Doctor and River's conversation up to this point.

"On it." The young Time Lady responded, chasing after River, leaving the Doctor alone in the console room.

It was at that particular moment, that the Doctor began considering possible destinations. He never did get his wish of taking a little holiday in Paris. But before he could continue that particular train of thought, the phone on the TARDIS console began to ring.

The Doctor moved over to the phone, and answered it. "Hello?" He spoke into the handset.

 _"Doctor, is that you?"_

"Shepard?" The Time Lord responded. "I don't remember giving you my phone number."

 _"The Normandy's comm systems have caller ID. But that's not important right now."_

"Then what is?"

 _"There's a derelict ship floating in the gravity well of a brown dwarf. I'm leading a team over to investigate, and I want you with us."_

"Really, that's it? You decided to go through the trouble of calling the TARDIS instead of waiting for me to come back because of an abandoned ship?"

 _"Doctor, it's not just any abandoned ship. It's a Reaper."_

"A Reaper?" The Doctor repeated, surprised, and just a little bit excited. "Are you sure that it's dead?"

 _"It's got a massive hole right through the middle. Yeah, it's dead."_

"Then send me the co-ordinates, I'll meet you there." He ordered, suddenly all-business. He still was a little bit excited, still. This was his first chance to study one of those things up close, and a prime opportunity to work out any weaknesses.

He just hoped it didn't backfire on them.

* * *

The TARDIS materialized in the Normandy's CIC, and the Doctor stepped out alone. He walked up the steps, and to the airlock, where Shepard, Zaeed, and Miranda were waiting.

"Finally." Zaeed said, as he and the others noticed the Doctor. "We can get this show on the road now."

"Alright, Doctor, here's what we're going to do." Shepard began, filling him in. "The IFF we need to get to be able to pass through the Omega-4 Relay is in that Reaper. Retrieving that IFF is the primary objective. While we look for it, I want you to examine that Reaper as much as you can. Look for chinks in the armor, so to speak."

"I planned on doing that anyway, to be honest." The Doctor admitted, shrugging.

"Then go right ahead." Shepard nodded. "But we all need to be careful. Even deactivated Reaper tech can indoctrinate people, and there's nothing suggesting that a dead Reaper itself is any different. We need to get in, do what we need to do, and get out as fast as we possibly can. Got that?"

"Understood." Zaeed and Miranda responded, while the Doctor just nodded.

"Then let's do it." Shepard stated. She walked over to the airlock controls, waited for the Doctor to put his breather mask on, and opened the airlock up. The team of four cautiously stepped out of the airlock, and into the Cerberus science facility that had been set up by the science teams.

The door to the facility opened up, revealing a corridor identical to the ones in other Cerberus facilities.

Bloodied handprints were on the wall, and a charred corpse lay on the floor, lifeless.

"Oh good, dead bodies, as if this place wasn't ominous enough." Zaeed sarcastically remarked, as he and the others moved forward.

As they moved forward, they came to a small lobby-like area, with a terminal on the wall. The terminal had a video ready to play, and Shepard pressed the play button.

"The airlock has been installed at the far end of the holled section." A middle-aged man stated, as the video flickered and distorted. "We have begun pressurization for shirtsleeves work. The crew is... on-edge. I reassure them that it is mere nerves. A superstitious reaction to what this place represents-the corpse of a vast and ancient life-form. Privately, I can't deny the atmosphere. The angles of the walls press down on you. I find myself clenching my teeth." With that final sentence, the video log ended.

"So, it looks like they _were_ being indoctrinated." Shepard noted. "We'd better not stay over here too long. Unless we want to end up like them."

The rest of the team nodded, and Shepard took point, leading the group to another airlock at the other end of the small room. They stepped inside, and the door slid shut behind them, as the airlock pressurized. The other door at the end of the airlock opened, but as it did so, the entire chamber rumbled and shook.

 _"Normandy to shore party!"_ Joker said over the radio, with just a hint of panic, almost immediately after the shaking started.

"What just happened?" Shepard inquired, holding her hand to the transceiver.

 _"The Reaper just put up kinetic barriers."_ Joker explained, as one of the Normandy's consoles beeped in the background. _"I don't think we can break through from our side."_

"Of course." Miranda shook her head.

"We're going to have to take the generators out ourselves." Shepard stated. She then turned her attention back to the radio. "Any idea where they are?" She asked of Joker.

 _"At the moment of activation, I detected a heat spike in what is likely the wreck's Mass Effect Core."_ EDI responded. _"Sending the co-ordinates now."_ Shepard's omni-tool flashed, confirming that it had received the co-ordinates. _"Be advised: The core is also maintaining the Reaper's altitude."_

"So we're gonna have to take it out, and then run like hell." Shepard sighed, and shook her head. "Why can't anything ever be easy for a change?" Then, she got back to business. "We're going to make a sweep for survivors, and recover what we can. Be ready to pick us up as soon as you get the signal."

 _"Uh... What signal?"_ Joker asked.

"You won't miss it." Shepard responded. She then closed the channel, and led the team forward. The large circular blast door opened, and the four stepped out of the Cerberus station, and into the Reaper proper.

Walking around inside the Reaper was... unsettling, to say the least. Even to the Doctor, who had faced down hordes of the most terrifying creatures imaginable. It felt as if at any moment the monstrosity could wake up, and eat them all. And as they walked along, the Doctor could _feel_ it pressing up against his mental barriers. Trying to get into his mind.

Then he realized: This Reaper wasn't dead. It was sleeping. No... _waiting._

"Doctor, you alright?" Shepard asked, a look of worry on her face.

"Yes, just a little... unsettled." He reluctantly admitted. "I think... I think it's watching us."

"The Reaper? But it's dead." Miranda reminded him.

"Its physical shell might be, but its mind... We should be careful." The Time Lord voiced. "If this thing is still conscious, who knows what it could do?"

"Husks!" Zaeed shouted, readying his weapon, and opening fire on the cybernetic creatures.

"Open fire!" Shepard ordered, firing her own weapon. The sustained fire of their weapons were no match for the husks, who had very little in the way of protection.

"Those were kind of weak, weren't they?" The Doctor asked, after the last husk fell.

"Husks are engineered to swarm in numbers." Shepard explained. "Distract their enemies long enough for the bigger foot soldiers to take them out."

"Makes sense." The Doctor stated. "So, where do you think this IFF is?"

"No idea." Shepard responded. "We're just going to have to fight our way through this place until we find it. Which I hope doesn't take too long. I don't fancy getting indoctrinated."

"Look at the design of this corridor." Miranda pointed out, looking at up at the ceiling of the massive hallway they were in. "This whole place looks like the inside of a circulatory system."

"Huh, you're right..." The Doctor agreed, looking at the walls. "I wonder what got pumped through here..."

"Whatever it was, it sounds like the Reapers are a bit more organic than they say they are." Shepard remarked. "Doctor, have you figured out anything useful from this thing?"

"According to this," The Doctor held up the sonic, "The Reaper's outer hull is made up of Element Zero. That's about as far as I got before the shooting started."

Shepard almost double-taked. "But that would mean this entire thing is just one giant Mass Effect core!"

"Not necessarily. Though the chemical makeup is identical, the _structure_ of the Element Zero in the hull is considerably different. Different to the point where the normal properties of the element no longer apply."

"But Eezo is so rare that building a ship this size entirely out of it would drain the supply of most of the major governments!" Miranda stated.

"Unless the Reapers figured out a way of engineering it artificially. They attacked Gallifrey in the past, if they got their grubby tentacles on the Hand of Omega..."

"Then they could make any star they wanted go supernova." Shepard finished. "Giving them an endless supply, as long at they have stars."

"I guess I'll have to go check after we get done here." The Doctor said to himself as much as the others of the group.

"But for now, we need to focus on the IFF." Shepard stated, as they proceeded deeper into the Reaper. Along the way, more Husks crawled onto the walkway, and attacked the four, like antibodies attacking a virus.

Eventually, the team came to a stop on a catwalk overlooking spikes arranged in a strange pattern.

"Dragon's Teeth." Shepard stated, looking at the spikes. "Guess we know where those Husks came from... and what happened to the scientists."

"Look at the way the spikes are arranged around that central part. It looks like they treated it as an altar of some kind." Miranda commented, examining the chamber.

"You mean they wanted this done to 'em?" Zaeed piped up from the back.

"If they were indoctrinated..." Shepard shivered. "Let's go, I don't want us to linger in case _we_ get indoctrinated as well." The three other team members nodded, and followed Shepard's lead. The Commander led them to an airlock, and they all sealed their suits, and put on their breather masks. The airlock equalized pressure with the high-pressure environment of the outside, and slid open, allowing the squad to exit, and walk around the outside of the Reaper husk.

Once on the exterior catwalk, Shepard gave the order for the squad to move ahead, before all of a sudden, gunshots rang out.

"Woah!" The Doctor yelled, diving to the ground.

Shepard, however, only heard the bullets as they whizzed past her ears, and impacted against something behind her. She turned around, faster than she ever had before, to see two dead husks, both with holes in their head, on the floor, the holes smoking.

Shepard turned back around, to the source of the sniper shot, to see a lone Geth stand up, and stare her straight in the eye.

"Shepard-Commander." The Geth vocalized, possessing a highly synthesized male voice. The Geth nodded, and turned away, disappearing deeper into the dead Reaper, leaving the four confused teammates to fend for themselves.

"Was that a _Geth!?"_ Zaeed nearly shouted, voicing the thought on everybody's mind. Everybody's mind, except for one.

"That was a Geth?" The Doctor asked, pushing himself up. "I didn't know they talked."

"They don't." Miranda answered. "Commander, there could be more nearby. Geth get considerably stronger in numbers... smarter too."

"Then we'll have to be on our guard." The Commander responded. "Let's continue moving forward."

The other three nodded, and followed Shepard, making their way along the catwalk installed by the Cerberus science team. Along the way, more Husks (along with the variant that exploded) crawled out from under the catwalk, and onto it, giving the team more trouble. The Husks were taken care of easily enough, thanks to the abundance of flammable materials in the battlefield.

But once the team got close to the next airlock, they encountered two Scions blocking their path. The two lumbering husks came out from behind a support beam, and let loose two powerful biotic shockwaves. Zaeed threw out an incendiary grenade, which burned through most of the tough armor on one of the Scions. Then, Shepard hit it with a shotgun blast to the head, causing it to go down, leaving the other Scion on its own. Miranda hit the other one with a Warp, and the Doctor used the Sonic Screwdriver to destabilize the molecular structure of the armor. Miranda then hit it again with another Warp, causing the Scion to be torn apart.

"Good work." Shepard complimented, leading her team into the airlock. The airlock began to equalize pressure with the inside, but while that was happening, Shepard's focus was drawn to a small piece of tech on a tiny desk. "The IFF." The Commander stated, picking it up. She felt it for a moment, before turning to the Doctor. "Think you can stash this in one of those pockets?"

The Time Lord nodded, and took the IFF, hiding it deep inside one of his jacket's many bigger-on-the-inside pockets. After he did that, the Sonic Screwdriver buzzed, causing the Doctor to examine it. He smiled once he realized what the confirmation bleep was about. "Scan complete! We can look it over when we get back to the ship."

Shepard simply nodded her agreement, and gave the order to ready weapons once the airlock got close to completing the cycling sequence. The door slid open, only for a glass barrier that covered the whole door to block the team's path. However, they could all still see out.

In front of what could only be the dead Reaper's mass effect core, the same Geth from before was typing away at a terminal, while three husks limped up behind it. The Geth then turned around, and let loose three shots, each one directed to the Husks' heads. Each shot hit its mark, causing the Husks to fall, and the Geth to get back to work.

"What the...?" Shepard breathed, staring at the Geth with barely-contained curiosity.

The Geth hit the enter key on the terminal, causing the glass barrier to slide down, allowing access into the core chamber. It turned around to address the group, but before it could vocalize anything, it was caught in the EMP blast of a Husk, causing it to deactivate.

"Open fire! Husks only!" Shepard ordered, unholstering her shotgun, and sending blasts into the crowd of Husks coming their way. "Doctor, do you think you could get the core shut down?"

"Sure," The Doctor responded, leveling the screwdriver at the open core, "let me just-!"

But before he could do anything, the open core discharged a blast of high-voltage static electricity, right at the sonic device. The electricity arced through the air, and collided with the screwdriver, frying it. The Doctor yelled, and dropped the screwdriver, as it smoked and shorted out. "Or not!" He quickly amended, picking the screwdriver back up, and stashing it in his pocket.

"Then we shoot it!" Shepard stated, firing a shotgun blast at the open core, causing some kind of blast shutters to close.

More Husks emerged from under the platform, and crawled on, trying to swarm the four. The team held their ground, however. Zaeed threw another incendiary grenade into the crowd, and it exploded, setting the Husks in the crowd on fire, burning them to death quickly. After this, the core shutters opened again, allowing Shepard to fire into the core again, making the shutters close once more.

Again, the Husks swarmed into a large group, trying to get close to the squad. Shepard, however, used this to their advantage. Activating incendiary ammo on her shotgun, she fired on the crowd of Husks, and watched as each one was set ablaze, either from the ammo, or the fire spreading. Afterwards, the core opened, giving the three with guns a clear shot.

The three's combined fire was enough for the core's containment shielding to break, allowing element zero to leak out, causing the mass effect field the core generated to dissipate, and the wreck to be sent down into the brown dwarf that it orbited.

With the core destroyed, Shepard ran over to the downed Geth.

"Commander, what the hell are you doing!? We need to get out of here before we're crushed!" Miranda shouted.

"That Geth saved me. I want to know why." The Commander determinedly stated, picking it up, slinging it over her shoulder.

"It's a Geth! We already have enough trouble!" Zaeed was quick to yell.

"This isn't up for negotiation." Shepard replied, leading the team into the airlock. The airlock opened, allowing the team outside. "Joker, we need pick-up, now!"

 _"Hold on, folks."_ The helmsman responded, as the four spotted the ship coming around,

"Open the main airlock." Shepard ordered. Then, the main airlock door slid open, allowing her to throw the Geth in. "Move it, people!" She yelled, jumping after the Geth. The others followed her, taking a running start, and leaping into the air, the low gravity allowing them to close the distance easily. Once the entire team was in, the airlock closed, and the Normandy flew away, leaving the dead Reaper to be crushed in the depths of the failed star...


	27. The Collectors Attack

After the risky mission of retrieving the Reaper IFF had been completed, Shepard, Miranda, Jacob, and the Doctor gathered in the meeting room.

"I think we need to discuss the unique piece of salvage we've recovered." Miranda instantly stated, getting into the discussion without ceremony. "For now, we've stored it in EDI's AI core."

"Hold on. You've got a Geth, known for their ability to hack just about everything, stored in the same room with the AI that controls the entire ship?" Shepard demanded. "What the hell were you thinking?"

"Relax, Commander. EDI's core has several hundred safeguards to prevent unauthorized tampering." Miranda explained. "The moment the Geth decided to hack EDI, if it were reactivated, it would be fried to a crisp."

Jacob, meanwhile, shook his head. "I say we should space it. Who knows what kind of tricks that thing has?"

"But imagine what could be learned from studying it."

"I'm talking to it." Shepard stated, staring at the Geth. "It knew me. I want to know why."

"Reactivating the Geth is a serious risk. If you do so, it should be for humanity's best interests, not your curiosity."

"I still think our 'best interests' involve an airlock." Jacob crossed his arms.

" _Thank_ you for your contributions, but it's my choice." Shepard reminded the two. "But I'll decide on that later. Right now, we need to discuss what we learned on the Reaper. Doctor?"

"Ah, right." The Time Lord coughed, stepping forward. "That blast from the Reaper's core fried the Sonic, but I did manage to recover the scans from the databanks." He said, tapping a command into a holographic keyboard, causing a hologram of the Reaper to be projected, along with data in Gallifreyan script alongside. "The exterior of the Reaper is nearly identical to scans you lot took of Sovereign when he attacked a few years ago. The outer hull is made of element zero alloy, blah blah blah... the _inside,_ that's where it gets interesting." He tapped the keyboard, causing the outer layer of the Reaper to vanish. "You know how Miranda said that tube we were in looked like a blood vessel? Turns out, she was right on the mark. It _was_ part of a larger circulatory system that ran the length of the entire Reaper. Here," A red blip was projected a little ways away from where the Reaper had a large chunk missing, "was where the central pump, or heart if you want, was located."

 _"Was?"_ Shepard repeated.

"That Reaper took a hit from a massive mass accelerator, yes? When that round hit, it ripped that section away. Along with the heart. _That_ was what killed it. Instantly too, it looks like."

"So that's our weak spot!"

"It looks that way, yes. The problem is; that area of the Reaper is so heavily armored, that it would take a mass accelerator ten times more powerful than the most powerful one in the galaxy to even make a dent." The Time Lord explained.

"What about high temperatures?" Miranda inquired.

"I _suppose_ a high enough temperature could melt the armor." The Doctor scratched his chin. "But I'm fairly certain this ship isn't carrying nukes with it."

"You know, the Turians are getting ready to put their 'Thanix Cannon' into mass-production." Shepard stated, looking at the Doctor. "Would that be enough?"

The Doctor thought about it for a moment. "It might be. I'd have to take a look at one to be sure."

"Garrus installed one a few days ago." Shepard explained. "You can go to him if you want to get the specifications."

The Doctor merely nodded.

"Now, onto the final order of business." Shepard began, bringing up a projection of the recovered Reaper IFF over the table. "EDI's scanned the IFF, and determined that it's safe to integrate with the Normandy's systems. So I'm having Tali and the others down in engineering working on it now.

"How long will it take?" The Doctor inquired.

"No more than a day." Shepard answered. "In the meantime, I'll get that Geth sorted out. You're all dismissed." She finished, exiting the room. On her way out, she grumbled something about "Tali's so not gonna be happy about this."

The others followed her example, and dispersed, going off to do their tasks for the day.

* * *

The Doctor, after having left the briefing room, down to the Main Battery room to get the tech specs from Garrus. Most of it was boring stuff, like rate of fire, reload time, and other stuff like that. The only thing the Doctor was interested in learning, was the temperature of the weapon.

"It shoots a stream of superheated liquid metal at a fraction of light-speed." Garrus explained, the Doctor paying attention to that part.

"How hot?" The Time Lord inquired.

"At _least_ six-thousand degrees Kelvin." Garrus answered. "Enough to get it white-hot. Why?"

"I'm the lead Reaper Weakness Finder." The Doctor smugly beamed. "It's my job."

Garrus blinked. "Is that the official title?" The Turian deadpanned.

"Er... no."

"It's not even an actual position, is it?"

"Yes! ...Well, no, but I caught Shepard's intent!" He then shook his head, and steered the conversation back on track. "Do you think it can melt through Reaper armor?"

"One of the cannon's first tests was against a chunk of armor recovered from Sovereign. It'll melt through Reaper armor."

"Right, good." The Doctor nodded. "I guess that means my job here is done. I'll let you get back to your calibrations." He said, exiting the main battery room.

On his way to the elevator, he couldn't help but stop and look into the sick bay, at the door that lead to the AI core. His curiosity got the better of him, and he wandered through the sick bay, into the AI core. It seemed that Shepard hadn't made her visit yet, as the Geth lay on a metal table, deactivated, behind a blue shimmering kinetic barrier.

He stared at the Geth for all of five seconds, before his desire to know more forced his next actions. "Hello, EDI, are you there?"

 _"I am always here, Doctor. What do you require?"_

"I don't mean to intrude, but could you, maybe, possibly, turn this Geth back on?"

 _"I am sorry, Doctor, but Commander Shepard has issued explicit orders to not re-activate the Geth until she has come to a decision on its fate."_

"I see..." The Doctor rubbed his chin. "EDI, isn't it true that I come from a parallel universe?"

 _"Yes."_ The AI honestly replied, not understanding where the conversation was going.

"And isn't it true, that Commander Shepard is an alternate version of myself?"

 _"That is correct."_

"Therefore: I _am_ Commander Shepard, aren't I?"

 _"...Authorization accepted. Re-activating the Geth."_

The Doctor smiled to himself. "Thank you, EDI."

Behind the shimmering blue barrier, the Geth stirred, and its optic glowed as it came back on-line. It planted its feet on the floor, and walked up to the barrier.

The Geth looked at the Doctor up and down, before speaking. "Doctor-Commander."

"...What?" Was the confused response the Doctor gave.

The flaps on the Geth's head pushed out, and the optic 'blinked.' "Runtimes active during platform incapacitation."

"Oh, so you heard that little spiel."

The Geth nodded, an oddly human mannerism for a machine. But then again, the Doctor had met machines far less advanced than this one, that were able to mimic human gestures with surprising accuracy. "Affirmative." The Geth shifted on its legs, correcting its imbalance. "Why have you reactivated us?"

"I was curious." The Doctor shrugged. "I'm not going to attack, if that's what you're worried about. Are you going to attack me?"

The Geth's optic dilated. "No." It answered.

"Good." The Doctor nodded. "Wasn't really worried about that, given that you helped us back on the Reaper. You also addressed Shepard by name. Do you know her?"

The flaps on the Geth's head flared again. "We know _of_ Shepard-Commander."

"Ah," The Doctor nodded, "she's fought you, so you know about her from the other Geth."

The Geth shook its head. "We have never met."

"Well, of course _you_ haven't. But there are other Geth that she's met."

"No." The Geth shook its head again. "We are all Geth, and we have never met."

"Wait a minute... You're software, aren't you?" The Doctor realized. "The thing that's pacing around in front of me is just a mobile platform."

"Correct." The Geth nodded. "Runtimes are downloaded into platforms upon requirement. When not in mobile platforms, runtimes are distributed within the Consensus. Runtimes then upload their recorded data to other runtimes."

"So like a digital gestalt. One of you learns something, the rest of you do as well."

"Affirmative."

"But, you haven't met Shepard?"

"Negative."

"That's confusing. She's fought Geth before." The Doctor thought back to Shepard's background. "On that colony, Eden Prime, and going after that Saren chap..."

The Geth tensed up, and its optic began rapidly spinning clockwise and counterclockwise. "Shepard. Commander." To the Doctor, it looked like it was accessing its databanks. "Human. Alliance. Fought Heretics. Rediscovered on the Old Machine." It relaxed, and its optic stopped spinning.

"Heretics, eh?" The Doctor repeated. "The Geth that she fought were ideologically different from your Geth?"

"Geth build their own future." The Geth answered. "The Heretics asked the Old Machines to give them their future. They are no longer part of us. We were studying the Old Machine to protect out future."

"So _that's_ why you were on the Reaper."

"Correct."

"And the Reapers are also a threat to you as well?"

"Yes."

"So it's not just organics they're targeting..." The Time Lord came to the grim conclusion. "They're going after everything. But why...?"

"We are different from them." The Geth answered, assuming the question to be about its species. "Outside their plans."

"So you _aren't_ allies with the Reapers?"

"We oppose the Heretics. We oppose the Old Machines." The Geth answered, stepping forward. "Shepard-Commander opposes Heretics. Shepard-Commander opposes Old Machines. Co-operation furthers mutual goals."

"You want to join the team?" The Doctor asked.

The flaps on the Geth's head flared out. "Yes." It nodded.

"Then what should we call you?" The Doctor asked.

"Geth." It answered.

"I mean you. Specifically."

"We are all Geth."

The Doctor sighed. "There's more than just _one_ runtime in that platform, isn't there?"

The Geth nodded, confirming the Doctor's statement. "There are currently one-thousand one-hundred eighty-three programs active within this platform."

"'My name is Legion, for we are many.'" EDI quoted, projecting her avatar next to the Doctor.

"I... _guess_ that works."

"Christian Bible, the Gospel of Mark, chapter five, verse nine." The newly named Legion recited. "We acknowledge this as an appropriate metaphor. We are Legion, a terminal of the Geth. We will integrate into Normandy."

"Hold it right there!" Commander Shepard ordered, storming into the AI core. "Doctor, what the _hell_ were you thinking!?"

"Well, it helped us back on the Reaper, so..." The Doctor sheepishly shrugged.

"Do you have any _idea_ what could've happened!?" The Commander scowled.

"You _were_ going to reactivate it anyway." The Doctor reminded her.

"Yes, but I was going to go that _after_ I put a security detail in here!"

"Oh... I messed up, didn't I?"

"A bit, yes." Shepard responded. She rubbed her temples, and said; "Alright, Legion, you aren't hostile, right?"

"Affirmative."

"Good." The Commander nodded. She brought up her omni-tool, and deactivated the kinetic barrier. "Welcome aboard." She welcomed, holding out her hand.

Legion looked down at the extended hand, and took it, shaking it. "We anticipate exchange of data."

"Oh, well, good!" The Doctor clasped his hands together. "That went as well as it possibly could've!"

"Given the circumstances, yes. But you really shouldn't have reactivated Legion without telling me!"

"How do you know his name's Legion?"

"EDI streamed the security feed live to my omni-tool."

"...Et tu, EDI?" Was all the Doctor could say.

* * *

"Do we really have to do this?" River groaned, as the Doctor led her out of the TARDIS, and up to the CIC.

"Yeah, a bit. Imagine if Shepard found someone new roaming around on the ship without warning. She'd think we'd been boarded!" The Doctor explained, pulling her into the elevator. "Plus, future her said we did, and I'd rather not have time rip apart. You understand."

"It's just that she's so... infuriating." River answered, clenching and shaking her fists. "So smug, cold, self-absorbed..."

"Obviously, you and I know two different Shepards." The Doctor remarked. "Just relax. It won't take long, and afterwards, we can go do whatever you like."

"Can we rob a bank on the Citadel?"

"No! ...Well, it depends. If people are in danger by _not_ robbing it, then sure." The Time lord answered, the elevator coming to a stop on Deck Two. The door slid open, allowing them to step out. Shepard herself was overlooking the Galaxy Map and frowning at something. "Shepard."

"Doctor." She responded, turning around. Her eyebrows raised once her eyes came to rest on River. "River?"

"Yes." The Doctor answered. Shepard was about to open her mouth again, but the Doctor beat her to the punch. "But she doesn't exactly remember you. Well, it's more like she hasn't met you at all yet."

"...More time travel stuff?"

"Bingo! This," The Time Lord gestured to River, who was standing a bit awkwardly to the side, "River, is freshly-regenerated!"

"Ah, got it." She nodded. "So, how'd it happen?"

The Doctor looked affronted. "Shepard, you can't just _ask_ that!"

"Why not?"

"...Let's just say, she's from the future."

"Right, the whole 'you should never know your own future' thing. Glad I watched Back to the Future." Shepard said, then she addressed River. "Welcome aboard, I suppose. If you need something to do I'm sure one of the crew members can help you out." Then, she turned back to the Galaxy map.

"...What are you doing?" The Doctor curiously inquired, looking at the Galaxy map.

"After you left the AI core, I talked to Legion myself. It said there was a station filled with Heretic Geth with a virus that could turn all Geth over to their way of thinking. Into believing that serving the Reapers was the best thing to do."

The Doctor's eyebrows raised sharply. "That isn't good."

"No, it's not." Shepard deadpanned. "I'm just pouring over the navigational data one last time. We're going to have to take the shuttle because of the IFF installation, so I want to make sure we won't be detected."

 _"Commander, the course is sound._ " EDI piped up. _"There is a ninety-nine point three percent chance you won't be detected by Geth sensors."_

"Ah, so I'm just being paranoid then. Well then, notify the team." Shepard ordered, stepping down from the Galaxy map, and into the armory. "I'll take who I want with me when we get closer to the objective. That means you have to come too, Doctor."

"Well, duty calls." The Doctor responded, following the Commander. "...I have a duty now?"

"I'm coming too." River said, following along.

"River-" The Doctor began, but was cut off by River holding her hand up.

"I've been waiting to get out and shoot something since I regenerated."

The Doctor turned to Shepard, causing the Commander to shrug in response. "As long as she can fight, it's fine by me."

"Oh, I can fight." River chuckled.

The door to the armory slid open, and Shepard walked inside, retrieving her armor from the locker. She suited up, and picked the weapons she wanted to take. She handed River a spare kinetic barrier generator, a shotgun, and a pistol, and Shepard led them back over to the elevator. They all stepped in, and Shepard hit the button to take them down to the shuttlebay, where the team was already waiting. Shepard gave the order to board the shuttle, and the team did just that.

The shuttle door swung closed, and the Normandy's shuttle bay door opened up. The shuttle lifted off the deck, and shot out of the bay, jumping to FTL towards its destination.

Meanwhile, a few decks above, Susan was assisting Doctor Chakwas in doing more bloodwork, with samples taken from Shepard and sneakily taken from the Doctor.

"Amazing..." Doctor Chakwas breathed, looking through a microscope at the sample. "I dosed these samples with enough radiation to kill someone stone-dead in five seconds. But it looks like they weren't exposed at all!"

"In Gallifrey's early history, something happened that caused our ozone layer to be stripped away." Susan began to explain. "Without it, we were much more susceptible to UV and cosmic rays, so we adapted."

"Well then, your species is remarkably well-adapted! You'd give the Krogan a run for their money in the resiliency department. Imagine what could be cured if we could somehow adapt the Regeneration process to work for all species..."

"Theoretically, anything." Was Susan's response. "As long as it didn't kill too fast. But then we'd have to expose everyone to the time vortex, and-" As Susan was in the middle of speaking, alarms started blaring, and red lights started flashing. Susan didn't know what the alarms were signaling, but it seemed that Doc Chakwas did.

"It's the intruder alert, we're being boarded!"

"Boarded!? By who?"

Just then, EDI gave an announcement over the ship's announcement system. _"Attention, all hands, the Normandy has been boarded by the Collectors. All hands prepare to repel boarders."_

Susan looked outside the sickbay's window, and saw the crew frantically grabbing weapons, and rushing to combat positions, but not all of the crew, it seemed. Susan, thinking fast, grabbed her own sonic screwdriver out of her pockets, and rushed out of the sickbay.

"Ms Chambers!" Susan ran up to the Yeoman. "You and the others without weapons have to get out of here!"

"But there's nowhere to hide!" Kelly rightly pointed out.

Susan looked around for a moment, and saw the port observation deck. "In there, I'll seal the door behind you!" She ushered, as the elevator began to come down to their level from the CIC. It could have only been filled with one thing-the Collectors. "Hurry!"

Kelly, along the others that didn't have weapons or just couldn't fight, was pushed into the observation deck. The door closed behind them, and Susan deadlocked it with the sonic screwdriver. It was then that she turned around, and saw Joker run out from Life Support Control, and across the deck, intent on making it into the sickbay for some reason.

Susan, deducing that he had a plan, ran to follow him, but as she turned the corner, a Scion grabbed her, making her drop the sonic screwdriver, her only means of defense against the hulking creature. Susan yelled out, shouting for help as the Scion pulled her into the elevator, and it and the other Collectors forced her into one of the pods they used. The pod sealed around her, and in moments, Susan lost consciousness...

* * *

Back on the shuttle, several minutes later, the shuttle's comm beeped, notifying them all of an incoming message. Shepard got up, and walked over to the comm panel, pressing the button to answer it. The message was text-only, and very short, but that didn't lessen the impact it had.

Shepard peeking into the shuttle's cockpit. "Pilot, turn this thing around!"

"Ma'am?" Was the pilot's confused response.

"The Normandy's been attacked by the Collectors! Get us back to the ship _now!_ "

"Aye, aye!" The pilot responded, turning the shuttle around, back on course for the ship.

On the entire ride back, the unrest and unease in the shuttle was almost palpable. About fifteen minutes later, the shuttle finally rendezvoused with the Normandy, and landed in the shuttle bay. The shuttle had barely landed, before the door opened, and the Doctor rushed out, frantically searching around for Susan.

"Susan!?" The old grandfather fearfully yelled, hoping beyond hope for a response. He took the sonic screwdriver out of his pocket, and set it to track Susan's. The device gave off a deep whirr which heightened in tone and pitch as he pointed it upwards, towards the upper decks. He ran into the elevator, and pressed the button to take him up. He went up a deck again once he realized that the other sonic was still above.

The elevator stopped on the crew deck, and the Doctor rushed out, following the sonic's change in sound to the other device. Eventually it led him right outside the med bay's door, upon whence he looked down, and fell to his knees.

His hand shook as he reached out and picked up Susan's sonic screwdriver, still warm from being held in her palm.

As Shepard walked up behind him, and tried to console him, the Doctor wanted to cry...

But all he felt was _rage._ Rage that some cruel force in the universe robbed him of a loved one. Rage that this had happened to him again. Rage that he let this happen to him again.

But most of all, a blinding, incomprehensible rage towards the Collectors.

He stood up, stashed both screwdrivers in his pockets, and stomped back to the TARDIS.

He'd get Susan back. But if the Collectors harmed her in any way...

They'd have Hell to pay.


	28. When A Good Man Goes to War

_They say that good men have too many rules. That isn't true. Good men don't_ need _rules._

 _And today, the Collectors were about to find out why the Doctor had so many..._

* * *

 _Somewhere, in the Time Vortex..._

The Meta-Crisis Doctor's TARDIS drifted through the Time Vortex, on an aimless course.

Ten himself was looking over the console readouts, while everybody else was lounging around, waiting for the TARDIS to land.

Then, he felt it.

Ten doubled over the console, breathing heavily. It was from the other Doctor, his progenitor.

Something had happened. He didn't know what, but he could feel it. The pure, unbridled rage that his counterpart felt. After a moment, the rage seemed to get under control, and that was when the phone on the console rang.

He walked over to the phone, and answered it. "Hello?"

 _"Susan's been taken."_ Was the no-nonsense response of the original Doctor. His voice was steely, and gone were the wacky mannerisms that he indulged in.

"Taken!?"

 _"The Collectors did it. I'm on my way to their base right now."_

Ten did a double-take. "You're what!? You can't just go in on your own!"

 _"Who says I can't?"_

"If you go in, trying to one-man army it, in an angry haze, you're going to wind up getting yourself killed!"

 _"I can just regenerate."_

"No, you _can't_! You used an extra regeneration to make me, and although we don't talk about _him_..."

 _"Argh, fine."_ The Doctor grumbled. _"What do you expect me to do then?"_

"...I bet you still have a few favors owed to you back home."

 _"Not a lot. I used up most of them when I went to Demon's Run-long story. But I think there's one person that might be willing to help..."_

Ten rubbed his forehead. "Look, just find someone to help. When you're ready, I'll be there to help."

 _"Thank you."_ The Doctor curtly responded, hanging up the phone.

Ten sighed, and sat down at the chair in the console room.

He _really_ hoped his counterpart knew what he was doing.

* * *

 _UNIT Headquarters. The Doctor's Universe. 1979_

The TARDIS materialized out in front of UNIT's HQ. The Time Lord peeked his head out, and smiled once he was satisfied that he was where he was supposed to be. He stepped out, shutting the door behind him, and made sure he had his UNIT ID.

He didn't particularly need it, given that he had the psychic paper, but you could never be too careful. He walked up to the front gate of the building, and was stopped by a young soldier.

"Sorry sir, but you can't enter without proper authorization." The Soldier stated, stopping the Doctor in his tracks.

The Doctor simply smiled, and produced the ID.

The Soldier looked at it, and stammered. "G-go right in, sir!" He saluted, then proceeding to open the gate.

The Doctor stashed the ID back in his pockets, and strolled right into the courtyard. He proceeded to enter the HQ, and remembering the path, walked to the Brigadier's office.

He rapped his knuckled on the door, and hearing "Come in." from the other side, he entered.

The Brigadier looked up from his work, and stared at the Doctor. "Good Lord, you've done it again!" He breathed in amazement. "I almost didn't believe Johnson when he said it was you... At the rate you're going, you'll turn into a child!"

The Doctor let out a tiny chuckle. "I wouldn't put it past me, knowing my luck."

"Hm." The Brigadier chuckled along. But it quickly dissipated, and the Brigadier got to business. "So, Doctor, what kind of alien threat has put the planet in danger this time?"

The Doctor flinched. "What? I can't visit an old friend from time to time?"

"Given that your social calls are usually followed by an attack of some kind, I have good reason to be worried."

The Doctor sighed, and shook his head. "No, it's nothing like that. My granddaughter, Susan, she's been kidnapped."

The Brigadier's eyebrows shot up. "Kidnapped? Who the devil would do such a thing?"

"An alien species called the Collectors, it's sort of a long story." The Doctor said. "The point is, the ship she was on got attacked by them while I was away, and they took her. I know where they took her, but if I tried to go in on my own..."

"So, you require UNIT's help for a change?"

"In a word: Yes."

"I'd be delighted to help." The Brigadier instantly responded, standing up. "Tell me where the enemy is hiding, and I'll do what I can."

"There's a problem with that... The Collector base isn't on Earth. It's orbiting a Black Hole. In another universe."

"Oh... Yes, I would say that is a problem." The Brigadier blinked. "But I'm assuming you have a plan?"

"...We could take the TARDIS, but I don't want to bring along more people than we have to. Breaking into that place is going to be a suicide mission."

"Doctor, most of UNIT's men have been trained to fight against impossible odds." The Brigadier retorted. "And they'd gladly go on a suicide mission if it meant helping you."

"You'd really go through all of that to help me?"

"Doctor, the human race as a whole owes you a debt of gratitude for saving the Earth time and again. If the time came for us to pay on that debt, we'd do it in a heartbeat."

The Doctor couldn't find the words to respond to that with. "I-... Thank you."

"So," The Brigadier began, getting back to business again, "what kind of environment can we expect to be fighting in?"

"If their main base is going to be anything like their ship was, then we'll be fighting in large, open spaces, with a lot of uneven terrain. It'll most likely have an oxygen-based atmosphere suitable for humans, but we can bring along rebreathers just in case."

"And the enemy itself?"

"Most of them are humaniod, but look a lot like walking bugs. Those ones are easy to deal with in small numbers, but some of them are armored more, and have better shielding. There are also cyborg-zombie things called Husks. They don't really have weapons, but if they get close, they can tear somebody apart limb from limb. The ones we really need to worry about though are the Scions and Praetorians. The Scions are a bit like tanks, slow moving, but they are hard to kill and pack a wallop. The Praetorians are flying tanks that can go invulnerable for a few seconds, fire a laser beam that can kill pretty much anything, and they slam the ground pulverizing anything under it."

"So, we need heavy weapons then?"

"Yes, heavy weapons. I can whip up some shield generators, too. And we'll need the Seeker Countermeasure, just in case..."

"It seems you have most of the mission planned out."

"Well, yes. We're waltz in and waltz out, but we've gotta be careful about it. There's another team being led by Commander Shepard. Her team is going to divert most of the Collectors' attention away from us while we go after Susan. After we rescue Susan from wherever she's being held, we head back to the TARDIS and get out of there, while Shepard and her team deal with the rest of the Collectors."

The Brigadier nodded his understanding of the plan. "In that case, a small strike team would most likely be effective."

"Probably. The Collectors will be too focused on Shepard's team to focus on us." The Doctor nodded. "But even still, it's going to be very dangerous."

"Doctor, danger is our specialty. Now," The Brigadier got up from his seat, and headed out the door. "I'll get a team assembled."

"And I'll head back to the TARDIS." The Doctor responded, leaving the office as well. He proceeded to walk back to the TARDIS, and moved it into UNIT HQ, waiting for the Brigadier to return.

After a few minutes of waiting, the Doctor heard knocking on the doors, and opened them up, allowing the Brigadier and four other UNIT soldiers to enter.

They were all packing some heavy firepower, which made the Doctor cringe a little. But, he conceded to himself, it was a necessary evil for the moment.

"Doctor, you've already met Sergeant Benton." The Brigadier re-introduced, causing the Doctor to smile and enthusiastically shake the Sergeant's hand. "This is Lieutenant Steward, Captain Brooks, and Corporal Shatner."

"Sir!" The three snapped off a salute, causing the Doctor to merely roll his eyes.

"Right!" He clapped his hands together. "You'll all want to hold onto something..."

The Time Lord ran over to the console, input the co-ordinates, and the TARDIS took off, breaching the dimensional barrier, and entering Shepard's reality...

* * *

Meanwhile, on the Normandy, things were no less tense. When Shepard looked into the Doctor's eyes after he discovered Susan was missing, she could feel his anger, his rage, and even a little bit of fear. At that precise moment, Shepard knew that the Doctor was going to the Collector Base, with or without the rest of them, and so she gave the order to prep the Normandy to head through the Omega relay.

"Are you okay, Shepard?" Garrus inquired, sitting down next to Shepard in the mess hall.

"No, truth be told, I'm terrified." Shepard replied. "Terrified of what we'll find, terrified of how the mission will go down, and terrified of what the Doctor will do if he can't rescue Susan. The Reapers are really playing with fire here."

"Oh? You really think the Reapers are going to be scared of a guy wearing a Bow Tie of all things?"

"I know it sounds silly, but... yeah." Shepard nodded. "When he first joined the team, I read up on the legends a little bit." She played with her drink for a few seconds. "Garrus, what does 'Doctor' mean to the Turians?"

"Almost the same as it does in the human language. Most of the time, we use it to mean 'Great Leader.'" The Turian answered.

Shepard nodded. "And isn't it strange how across all these different languages, 'Doctor' is the one word that seems to be universal?"

"Now that I think of it... What exactly are you trying to say?"

"I'm saying that every species, and I mean _every_ species, has a legend of some 'Doctor' man who just dropped out of the sky one day, defeated a great evil that was threatening their world, and that's where they get the word 'Doctor.' If even _one_ of those is true... then the Reapers should be afraid. They should be very, _very_ afraid."

* * *

 ** _This is super short, I know, and I apologize, but writer's block hit me like an oncoming truck driving down the wrong end of traffic. But, next chapter, things kick into high-gear, the Doctor has a conversation with the Collector General, and Shepard learns just why the Collectors are taking humans._**


	29. Demons Run

"Okay, everyone." The Doctor began, stepping out of the TARDIS first. "Here we are." He took in a deep breath, and looked out on the Collector base. The entire place was massive, and certainly similar to the Collector Ship in design. He took out the Sonic Screwdriver, and scanned around. His face instantly brightened. "I found Susan! She's being kept in a chamber near the heart of the station. If we go in that," He pointed to a corridor to the northeast, "direction, we can get to her in about five minutes."

"Then we'll go in that direction." The Brigadier stated. "Brooks, Shatner, cover our rear. Steward, Miss Song, watch our sides. The Doctor and I will take point. Let's move out!"

* * *

Meanwhile, across the base, the Normandy had crashed in a spot close to an open entrance into the base, After determining their next course of action, Shepard lead a small team alongside a vent, while Legion climbed through. The vent would allow Legion to open a locked blast door that led deeper into the base from the other side, ensuring that the team could get closer to the center of the station. The Collectors were firmly determined to ensure that the team wouldn't succeed, however.

But that didn't stop them from trying. Shepard's team continually pressed forward, plowing through the Collector forces that stood in their way. Eventually, the team came to the door.

On the other side, Legion was trying his best to bypass the Reaper code, but the door was being stubborn, adapting to his efforts to open it up. Finally, the Geth succeeded, and the door opened, allowing the team to enter. Once everyone was through, the door shut, and they caught their breath.

"Shepard," Miranda addressed, looking to the other end of the room, "Look." She pointed.

Shepard turned around, and saw her. "Susan!" She ran up to the pod, and in an act of pure emotion, shattered the transparent barrier cutting off Susan from the rest of them.

"Grand... Grandmother?" Susan mumbled, falling against Shepard.

"It's okay, I'm here, you're safe." She rubbed Susan's hair. But quickly, the reunion was broken up, as she looked at the other pods.

Inside, there was another woman. Her eyes snapped open, and she looked around the room with fear.

"She's still alive." Garrus commented.

But then, things only went downhill. The woman's skin started to be stripped right off her body, and she started collapsing into a grey paste.

"Get everybody else out of those pods, now!" The Commander shouted, setting Susan down to aid the rest of the team. They all bashed against the barriers of the pods, and pulled whoever they could out before they could be converted as well.

"Doctor Chakwas, are you okay?" The Commander worriedly inquired.

"Shepard. You... you came for us."

"No one gets left behind." Shepard stated, pulling Chakwas to her feet.

"Commander, you're here..." Yeoman Chambers clutched her sides as she limped along. "A few more seconds, and..."

"I dare not think about it." Chakwas finished. "The colonists were... processed. Broken down by nanomachines into some kind of grey paste, and then pumped through those tubes. At least, I think so."

"Susan!" The Doctor suddenly burst in, and ran over to the young Time Lady."You're okay..." He hugged her. "You're okay."

"A few seconds later, and she wouldn't have been." Shepard said. "The people in the tubes were turned into some kind of liquid, and pumped out to who knows where."

The Doctor's face instantly darkened.

"But why...?" Shepard wondered, looking up at the tubes. "What are they doing here?"

"It doesn't matter." The Doctor stated. "We're going to stop them. Susan, head back to the TARDIS, I might need her on a moment's notice. The corridor we came down is safe, totally empty."

Susan nodded, and got up. "Okay..." She walked back down the corridor the Doctor came from, and proceeded back to the ship.

"Those tubes are all going in a single direction." The Doctor pointed out. "So they must lead somewhere. Most likely whatever they're using this stuff for. You lot need to follow them."

"Hold on, 'you lot?'" Shepard repeated. "And what are _you_ going to be doing?"

"I've got backup incoming. Us" He gestured at the UNIT soldiers, "and the rest are going to find a control room, and try to get some useful info from it."

"Okay, but make sure you keep your omni-tool tuned to the right comm channel. Once we set this place to blow, there's no turning back."

"Got it." The Doctor nodded.

"Then let's all move out."

* * *

The Doctor's sonic screwdriver whirred as he pointed it in different directions. Once he pointed it roughly southeast, it changed pitch and started to rapidly beep. "The control room's that direction. I'm going to have me a few words with whoever's in charge."

"Doctor, doesn't this seem to be a bit too easy to you?" The Brigadier inquired.

"Nope!" The Time Lord cheerily responded. "My other self is drawing the Collectors away for us, along with Shepard, so the path is clear."

"What do you expect to find?"

"No idea!" The Doctor seemed chipper at that. "But there's the door, so we'll find out soon enough. Give me a second." He ran the sonic over the door, and frowned slightly. "Oh, you cheeky little... The Collectors have adapted to the sonic screwdriver, found a way to guard against it. Still, won't stop me." He determinedly stated, as the door slid open. He smiled, stowed the screwdriver, and proudly strode in. "Hello then, ladies and gents!" He yelled, wanting to make as much noise as possible. "The Doctor will see you now! ...Wait, I've said that before, haven't I?" He shook his head, and strode over to the Collector general. The General was significantly more insect-like than its brethren, possessing multiple legs, and a shorter, flatter stature. "Now, you've been a very naughty boy, haven't you?" The Time Lord quickly grew serious. "Why are you abducting people? What for?"

 **"OUR MOTIVES ARE BEYOND YOUR COMPREHENSION."**

"Oh, I dunno 'bout that. I'd say I'm a pretty clever guy." The Doctor responded, staring the Collector dead in the eyes. The eyes were glowing with intensity, but they were soulless, empty, the controlling intelligence truly behind them long since gone. It was then that the Doctor realized what had been going on all along. "Of course, the Collector's aren't really the ones responsible, are they?" He said, turning to point at the hologram the Collector was staring at. "You are. So... Harbinger, as you seem so intent on calling yourself, why?"

 **"ORGANIC LIFE IS NOTHING MORE THAN A GENETIC MUTATION. CHAOTIC LIFEFORMS BENT ON DESTROYING THEMSELVES AND THEIR SURROUNDINGS. WE WILL BRING ORDER TO THAT CHAOS. WE WILL BE YOUR SALVATION THROUGH DESTRUCTION."**

"See, that's where you're wrong." The Doctor responded. "Yes, you _could_ destroy all organic life, but you always leave the younger species alone. Allowing them to thrive and reach space travel on purpose to harvest them. And to harvest means that you've been cultivating something. You've been cultivating for a very long time, too, but what for...?"

 _"Doctor."_ Shepard's voice suddenly came out of his onni-tool. _"The people that were melted down... The Collectors are using them to make a Reaper. We're going to destroy this thing and set the place to blow. On my signal, you need to get out of here."_ Then, the channel cut.

"So, _that's_ what you're doing. Every fifty-thousand years, you come and harvest, processing the species that fit your criteria into a Reaper." The Doctor deduced, glaring sharply at the Reaper. "The only reason you would do that, is if you were building your strength to fight something. Something worse than you lot. What is it?"

 **"AT THE BEGINNING OF TIME, WE GAZED FORWARD, AND SAW ONLY DARKNESS. SILENCE. THE END OF ALL THINGS. WE WILL PREVAIL. WE WILL SURVIVE."**

The Doctor went white as a sheet. "Silence..."

 **"SILENCE WILL FALL, AND WE WILL PERSIST. THE CYCLE WILL CONTINUE."** The Reaper vowed, as the hologram disappeared. The Collector General collapsed to the floor, lifeless.

 _"Doctor, I've set the charge, you need to get out!"_

"Got it!" The Time Lord responded, running over to a control panel. He transferred all of the data to the TARDIS, and led the others out of the room.

The Doctor pulled out a walkie-talkie, and contacted his duplicate. He told the younger Doctor to get out of the base, and soon after, heard the sound of a TARDIS dematerializing. An explosion rocked the base, and fires broke out all around them. "Quickly, this way!" He guided, running back to the TARDIS landing spot. Upon the snap of the Doctor's fingers, the doors swung open, and all of them made it inside. The Doctor closed the doors, and he set the TARDIS into flight, taking off just as the spot where they previously were burst into a giant fireball...

* * *

"Woohoo!" Shepard and the rest of the crew cheered. "Who's like us!?"

"Damn few!" The Normandy's crew shouted in response.

"And they're all dead!" She yelled back. "We still have a few things we need to take care of, but tonight, we party!" She proclaimed, the crew cheering once more. Shortly after their victory over the Collectors, the crew felt the collective desire to throw a big damn party and get smashed.

Everyone except for the Doctor, that is. About two hours into the party, Shepard still hadn't seen hide nor hair of the older Time Lord, even though Susan was on board keeping an eye on Doctor Chakwas.

"Doctor?" Shepard asked, stepping into the TARDIS.

"Oh, hello Shepard." The Time Lord responded.

"What are you doing?" Shepard inquired.

"I'm just finishing the transfer of data I picked up from the Collector base." The Doctor answered, staring at the monitor on the console. "It won't be much, but it'll definitely help."

"That's it?"

"Yep, that's it." The Doctor responded. "After this is finished, I'm going to try to figure out more about the Reapers, where they came from, who built them... why."

"So... you're leaving?"

The Doctor absently nodded. "The data included approach vectors of the entire Reaper fleet. I've tracked their point of origin back to the Large Magellanic Cloud. I'm going to go there, find the people that originally created the Reapers. If they're still around."

"And what about Susan?"

The Doctor shook his head. "She's not coming along. I nearly lost her once. Not again. And River'll need someone to keep an eye on her as well."

Shepard shifted on her feet, and crossed her arms. "I know what you're trying to do. It isn't healthy, you know."

"I don't care. Who knows what I'll find in the LMC?" The Doctor shook his head. "Nope. It's too dangerous for them to come along."

"Fine then, just... be careful."

The Doctor smiled. "When am I ever not?"

* * *

 ** _And with this, the Mass Effect 2 arc ends, but the mission to the Collector Base only raises more questions. The most pressing (for me, at least) being, what will the Doctor find because of his trip to the LMC?_**

 ** _This chapter does not signal the end of this story. In contrary to what I had planned earlier, this story will continue into Mass Effect 3, instead of being a separate work, so if you're still interested, keep your eyes out for the next chapter._**


	30. Priority: Earth

_In the intervening months after the destruction of the Alpha Relay and the Reapers arrival, the Alliance did everything they could to prepare for the Reapers' arrival. But alas, the element zero based technology that all species in the galaxy made use of forced the Alliance to develop technology along paths that the Reapers could anticipate. Nothing any species could develop would be able to destroy them._

 _Which meant that the only hope for survival lay on the planet Edom, in the Large Magellanic Cloud. The homeworld of the Reapers._

* * *

The TARDIS materialized on a craggy overlook, overlooking an expansive desert with very little life. The Doctor stepped out of the TARDIS in his Sanctuary Base Six spacesuit, a necessity as the atmosphere of Edom was primarily nitrogen-argon, with no oxygen at all. The alien world had very little gravity, allowing the Doctor to jump off the overlook and gently float all the way down to the bottom of the cliff.

Upon his arrival in the LMC, the Doctor discovered an ancient space station, similar in design to Reaper structures. After accessing the database, a map was projected, showing an entire network of bases and outposts, with Edom at the center.

The entire planet was ruins, abandoned by the long-since extinct inhabitants.

The Doctor climbed up a large hill, opposite of the TARDIS, his foot almost slipping off the sandy footholds multiple times. When he finally got to the top, the Doctor laid his eyes on something that confirmed his suspicions.

Up in orbit, so far away that it looked like a thumbtack, though still visible, was an identical counterpart to the Citadel in the Milky Way. This was the planet that the Reapers retreated to in between the cycles, and that duplicate Citadel was the relay they used to travel to and from the Milky Way.

According to the TARDIS's scans, the entire planet was one massive scorched desert, but ruined cities scattered the surface. The one in the distance, directly under the Relay, was the largest, and maintained city, which the Doctor proceeded towards.

Upon arriving, the Doctor noticed something curious. A Time Lord scientific outpost. The outpost was ancient, predating TARDIS technology, but perhaps there was something inside he could use. The Doctor entered the research outpost, only to find that most of the tech inside was completely fried, save for only a single data storage drive. Picking up the storage drive, he took it back to the TARDIS.

After reentering the TARDIS, the Doctor plugged the storage drive into a slot on the console in order to access the data on it. Upon achieving access, the TARDIS projected a hologram of some kind of device.

The Doctor stared at the projected components with wonder. "Brilliant... Absolutely brilliant!"

* * *

Meanwhile, on Earth, Shepard sat in an Alliance prison cell deep within the main Alliance Headquarters building in Vancouver. Shepard looked out the window at a rooftop park, where a little kid was playing with a toy fighter.

Abruptly, the door to her cell open, and James Vega strode in. "Commander." He saluted.

"You aren't supposed to call me that anymore, James." Shepard pointed out.

"I'm not supposed to salute you either." The marine returned. "We have to go. The Defense Committee wants to see you." He said, leading Shepard out of the room.

"The Committee?" Shepard repeated, raising an eyebrow. "What for?"

"Don't know." Vega honestly replied. "Just said they needed to speak with you. Now."

As Vega led her to the Defense Committee's meeting room, they passed into a large crowd of Alliance officers. One stood out in particular.

"Anderson." She greeted, shaking the Admiral's hand.

"Admiral." Vega saluted.

"You look good, Shepard." Anderson greeted, leading them back the way he came. "Maybe a little soft around the edges. How are you holding up since being relieved from duty?"

"Well, it's not bad once you get used to the hot food and soft beds." The Commander responded.

"We'll get it sorted out." The former Councilor promised.

"What's going on?" Shepard asked, after a sprinting officer nearly ran into her. "Why's everyone in such a hurry?"

"Admiral Hackett's mobilizing the fleets." Anderson answered. "I'm guessing word's made it back to Alliance Command. Something big's headed our way."

Shepard stopped at the bottom of a set of stairs. "The Reapers?"

Anderson turned around to look at her. "We don't know, not for certain."

"What else could it be?"

Anderson shook his head. "If I knew that..."

"If it is them, we're not ready." Shepard stated. "Not by a long shot."

"I know. Without the Doctor here, we've lost our ace in the hole. But try telling that to the Defense Committee." Anderson said, continuing forward.

"Unless we're planning to talk the Reapers to death, the Committee is a waste of time."

"They're just scared." Anderson covered. "None of them have seen what you've seen. You faced down a Reaper. Hell, you spoke to one, then blew the damned thing up! You've seen how they harvest us... what they plan to do to us. You know more about them than anyone."

"Is that why they grounded me?" Shepard asked. "Took away my ship?"

Anderson stopped to point at Shepard. "You know that's not true. When you destroyed the Alpha Relay, thousands of Batarians died."

"It was that, or let the Reapers walk through the back door."

"I know that, Shepard, and so does the Committee. If it weren't for that, you would've been court-martialed and left to rot."

"That, and your good word?"

"Yeah, I trust you, and so does the Committee."

Shepard sighed. "I'm just a soldier, Anderson, no politician."

"I don't need you to be. I just need for you to do whatever the hell it takes to make sure the Reapers are stopped." Anderson led them into the waiting room, and they walked over to the entrance proper.

"Good luck in there, Shepard." Vega wished.

Shepard nodded, and her eyes followed him down the hall as he disappeared. As she turned back around to face Anderson, out of the corner of her eye, she saw something... familiar, but as soon as she turned to get a better look, it vanished.

"Shepard." The voice of Kadian Alenko grabbed her attention.

"Kaidan." She approached to stand next to Anderson.

"How'd it go in there, Major?" The Admiral questioned.

"Okay, I think." Kaidan shrugged. "Hard to know. Now, I'm just waiting for orders."

Shepard's eyebrows raised. "Major?"

"You hadn't heard?" Anderson asked.

"No." Shepard shook her head. "I'm a bit out of the loop."

"Sorry, ma'am." Kaidan apologized.

"You don't need to apologize." Shepard returned, though still a little bit hurt on the inside from Horizon. "I'm sure you had your reasons."

"Yeah... I suppose."

"Admiral," The Secretary addressed, "They're ready."

"Then let's not keep them waiting."

* * *

The Commander and Anderson walked into the Committee's meeting hall, and stopped in front of the Committee heads.

"What's the situation?" Shepard asked, proceeding directly to the point.

"We were hoping you would tell us." A bald Admiral responded, as an aide handed Shepard a datapad.

"The reports are unlike anything we've ever seen." Another Admiral began. "Entire colonies have gone dark. We've lost contact with everything beyond the Charon Relay."

"Whatever this is, it's incomprehensibly powerful."

Shepard stopped reading the datapad's contents, and let her arm fall to her side. "You brought me here to confirm what you already know..." Shepard began. "The Reapers are here."

"Then... how do we stop them?"

"Stop them?" Shepard repeated. "There's no stopping them. No ship, no fleet could hope to even put a dent in one of them. Now, we're just living on borrowed time. The Reapers are more powerful than us. Smarter, more intelligent. They won't take pity on us, and they don't fear any of us."

"But... there must be _some_ way."

Shepard started pacing. "No one species in the galaxy can hope to stand against the Reapers on their own, save for one... The Time Lords."

"The Time Lords!? You'd put the galaxy's survival on nothing more than boogeymen?"

"The Reapers were boogeymen just a few months ago." Shepard fired back. "The entire galaxy nearly came to be under Time Lord rule, until they retreated. They didn't do it because they were close to losing, or they were running dry on resources, they did it because they had gotten _bored_ of the war. They can destroy entire star systems at will, and they stopped because their Lord President decided that they'd get more entertainment from watching Soap Operas. With them on our side, the Reapers won't just be defeated. It'll be like they never existed in the first place."

"That's it!? That's our plan!?"

"Admiral," An Ensign from the back spoke up, "We've lost contact with Luna."

"The moon?" Anderson whispered. "They couldn't be that close already."

"How'd they manage to get pass our defenses?"

"Sir," The same Ensign from before said, "UK Headquarters has a visual."

"On screen." Anderson ordered, turning around to face the large monitor mounted on the wall.

The screen filled with static for all of about four seconds. Slowly, the static cleared showing an Alliance Marine in front of a burning building, trying to deliver a report on the situation, but the sounds of gunfire and fighting in the background made it hard to hear.

Suddenly, the sound of a Reaper reverberated out of the speakers, and the camera shook, falling to the ground. A split second later, the signal dropped.

Another second later, news coverage filled the screen, live feeds of Reapers all across the Earth were projected on the screen. The image froze on the clearest view of the Reaper, showing it touching down in New York.

"Why haven't we heard from Admiral Hackett?" Anderson wondered. Either the Reapers were jamming all communications on the planet, or Hackett was dead. Both possibilities weren't encouraging.

"What do we do?" An Admiral asked.

Shepard turned around to stare the Admirals dead in their eyes. "The only thing we can. We fight, or we die."

After Shepard said that, a loud noise, somewhere between a growl and the sound an airplane makes when it flies, reverberated throughout the room.

"Oh my God..." An Admiral breathed with horror, staring out the window.

Outside, red lightning flashed in the clouds, heralding the arrival of a Reaper. As soon as it descended below the cloud cover, the Reaper opened fire, a red beam of molten metal shooting out with a hellish _'fwaamp.'_

"Move!" Shepard yelled to all in the meeting hall, once she realized the fire from the Reaper's weapon was heading straight for them. "Go, go, go!"

The massive window in the meeting hall shattered, and the large desk the Admirals were previously sitting at was thrown across the room, as the Admirals themselves were incinerated from the heat of the weapon. The desk flipped, and broke against the wall, Shepard having ducked to dodge it. Another discharge from the Reaper's main weapon lanced out, and another explosion rocked the building, which threw Shepard against the wall.

"Shepard!" Anderson called, running over to the Commander. "Come on, get up." He ordered. Shepard extended out her hand, and he grabbed onto it, pulling her up. "Here, take this." He ordered, holding out a pistol to her. "We've got to keep moving." Shepard took the pistol, and followed Anderson to the shattered window. "This is Admiral Anderson, report in. Anyone?" He spoke, activating his comm. "Major Alenko, is that you? What's your status?" Anderson paused while he absorbed the information. "I can't raise the Normandy. You'll have to contact them. We'll meet you at the landing zone. Anderson out."

The two stopped, looking out over Vancouver. It had only taken the Reaper several seconds to level several city blocks, and set fire to numerous buildings. Shuttlecraft and fighters whizzed by as they tried to evacuate and fire upon the Reaper. Several other Reapers had also made landfall, and had begun their own destructive actions.

Anderson peeked over the edge, and saw the catwalk. Anderson nodded to Shepard, and they both jumped down.

When they hit the catwalk, they immediately proceeded along, in the general direction of the spaceport.

While they were walking, Shepard started fiddling with her omni-tool, trying to pick up any comm traffic.

"Anderson," Shepard addressed, once her omni-tool received a signal, "listen."

 _"Alliance personnel, please stand by for an emergency flash-traffic message."_ The automated announcer of the Alliance EBS stated. The voice then switched to a man's, due to the live transmission. _"This is a galaxy-wide alert for all human territories. Fleet Admiral Steven Hackett has declared threat condition Saber One. Enemy presence confirmed in Sol System. Earth under Reaper attack. I say again: Reaper attack is underway._ " The comm signal got choppy and staticy when a Reaper boomed, but quickly leveled out. _"...further instructions to follow on coded channel Crimson Tacit. May God save us."_

"Sounds like Hackett survived the initial attack." Shepard stated, as they moved along, killing Husks that got in their way.

"But if he's declared Saber One, then things are a lot more worse than we thought."

"How worse?" Shepard questioned.

"All government leadership for the Alliance has been killed, we've lost Arcturus, and the home fleet's been decimated." Anderson answered, as they approached a flaming building that took a hit from a Reaper weapon.

"Damn." Shepard cursed. "It's going to be hell trying to organize a counterattack." They entered the flaming structure, and Shepard walked up to a malfunctioning door. She forced it open, and held it. "Through this way." She said, letting Anderson go through. She was about to go through herself, when the sound of clanging metal brought her attention elsewhere. She looked to her right, and what she saw made her go pale. "...Ash?" She whispered.

"Shepard." Anderson called, turning Shepard's attention to him. "We need to keep moving."

Shepard looked back, and the phantom was gone. Shepard shook her head, and followed Anderson.

"This is a goddamned mess." The Admiral growled, shifting a chunk of debris out of their path. "Every minute those things are here, thousands of innocent people die. We can't let that happen."

"I know." Shepard responded, pushing aside another chunk. "But unless we find something to take them out with..."

Anderson sighed. "They hit so fast... I thought we'd have more time."

"Still, we knew they were coming."

"And yet, they just cut through our defenses." Anderson shook his head. "We need to go to the Citadel." He stated, climbing over a metal beam. "Talk to the Council."

"The Citadel?" Shepard repeated. "The fight's here."

"It'll be everywhere soon enough." Anderson replied, beginning to inch along a catwalk that had mostly been taken out by falling chunks. "You said it yourself... The Reapers will destroy everything unless we stop them, and unless you can guarantee the Time Lords will intervene... Rallying together all our forces will be our best shot."

The building suddenly shook, and Shepard lost her balance, falling forward. Just before she fell, Anderson grabbed onto the back of her uniform, and pulled her back over the edge.

"Thanks." Shepard breathed, continuing along. "I owe you one."

"More than one." Anderson replied, as they both got to a safer point. "Let's go." They both jumped back out of the building, onto the ledges on the outside. Directly in front of them, in the bay, another Reaper landed, opening fire on the city. "Major Alenko, we're in sight of the spaceport. ETA: 3 minutes.

 _"We've made it to the Normandy, taking heavy fire-oh shit! They're going to take down that dreadnought, evasive maneuv-!"_

"Major!?" Anderson repeated. "Kaidan! Damn it, they're in trouble."

The Reaper that had landed opened fire on a nearby cruiser, the red beam of molten metal cutting through the cruiser's hull like wet tissue. One final shot caused the cruiser's reactor to go critical, and explode, sending out a massive shockwave that caused the walkway Anderson and Shepard moved along to collapse, sending both soldiers to fall. Fortunately for them, they were sliding down the side of a building at an angle, instead of straight down, meaning the worst they got from the fall were a few bruises.

"Normandy, we're going to re-route." Anderson stated, getting up. "Do you copy?" The only response he was met with was static, and Kaidan's broken and stuttering voice, too unintelligible for Anderson to get any meaning. "Normandy? Damn it!" Anderson cursed, cutting the link. "We're going to have to find a radio."

"Look," Shepard pointed, to a Marine pinned under a chunk of debris and the medic tending to him, "Friendlies." She jumped down, and approached them. "You two alright?"

"Shh!" The medic shushed. "Get down! They'll see you!"

On the other side of the stream, three husk-ified Batarians screeched, and opened fire upon Shepard with weapons integrated into their arms. Shepard and Anderson returned fire, Shepard sending out a few incineration blasts to burn the Batarian Husks to ash. Once the threat had been cleared, Anderson and Shepard moved to opposite sides of the chunk of debris, and lifted it off the Marine. The debris sunk into the water, but enough remained above the surface to act as a bridge.

"Come on." Anderson took point over the bridge. "That gunship's got to have a radio."

Shepard nodded, and followed. In their way were three more Husked Batarians, but those were easily dispatched. After the immediate threat was taken out, Shepard and Anderson ran over to the downed gunship. Lucky for them, there was already radio on the ground, next to a dead Marine.

Shepard picked up the dead Marine's assault rifle, while Anderson tried to get the radio working.

"Normandy, this is Anderson, do you read?" The Admiral said, fiddling with the radio's controls.

 _"Admiral?"_ Kaidan responded. _"What's your location?"_

"By a downed gunship in the harbor." Anderson answered. "I'm activating its distress beacon. Shepard and I are going to hold position, and wait for evac." Only garbled static was the response. "Major? Damn," He smacked the radio on its side, "Lost the signal."

"Let's hope that beacon does its job." Shepard said.

"And fast." Anderson pointed to the sky, where Reaper Drop Pods were inbound to their position. "We've got company!"

The pods hit and dispersed their cargo, more of the Batarian Husks. Shepard and Anderson dove into cover, and opened fire, taking each one out with surgical precision.

"Hope they get here soon!" Anderson yelled, shooting one of the Batarian Husks in the head, causing it to fall.

"You and me both!" Shepard responded, sending out a few incineration blasts.

More drop pods sped down from above, crashing and releasing more Reaper troops.

"I'm running out of ammo!" The Admiral shouted, taking out one last Husk before his pistol started clicking.

Shepard ran out of ammo herself, and switched to using tech powers instead. But before she could send out even one incineration blast, the most beautiful sound she'd ever heard filled her ears.

 _"Calvary's here, gentlemen!"_ Joker snarked, flying the Normandy directly over the battlefield. The ship fired a few missiles, which hit and detonated in a large group of enemy troops. The Normandy then swooped over, and held position near a bit of debris sticking out of the ground like a ramp.

"Bout time!" Anderson responded.

"Let's go." Shepard said, running towards the ship.

The Normandy got closer to the makeshift ramp, and the shuttle bay door opened downward, allowing Shepard to jump on board.

"Welcome aboard, Shepard." Kaidan greeted.

"Thanks." The Commander returned.

"Shepard." Anderson addressed, stopping at the top of the ramp.

"Come on!" Shepard ushered for Anderson to jump aboard.

A shuttle flew overhead, and touched down near a large group of civilians. "I'm not going." Anderson stated, looking at the shuttle whiz by. "You saw those men back there. There's a million more like them, and they need a leader."

"If you're staying, so am I." Shepard responded.

"The hell you are!" Anderson shouted back. "This is a fight we can't win! Not without help. We'll need every species, and all of their ships, to even have a chance of defeating the Reapers. You need to go to the Citadel, talk to the Council."

"Me!?" Shepard incredulously shouted. "I warned them about the Reapers years ago, what makes them think they'll listen now!?"

"Then you _make_ them listen! Now go, that's an order!"

Shepard snorted. "I don't take orders from you anymore, remember?"

Anderson looked down at something he held in his hands, and threw it to Shepard. Shepard caught them, and looked down at them, realizing they were her old dog tags. "Then consider yourself reinstated... Commander."

Shepard sadly looked down. "I'll be back... And I'll bring every fleet I can." She vowed, moving to step behind the yellow safety line in the shuttle bay. She turned back to look at Anderson. "Good luck." She wished.

"You too, Shepard." Anderson nodded.

With that, the Normandy began to lift off, leaving Anderson behind. Anderson ran back down the ramp, and Shepard turned to look at the large gathering of civilians. Who she saw standing in the center made her blood run cold.

Ashley Williams stared back at Shepard, dead in the eyes. The loud blaring of a Reaper Destroyer caught Shepard off guard, causing her to jump slightly. The Reaper charged its main weapon, with the intent of opening fire on the large gathering of people. The people scrambled to get in the shuttles, which took off not one second after everyone was on Reaper stepped on the ghostly apparition, and fired on the shuttles, tearing them to shreds.

The Normandy's shuttle bay door closed, blocking the view of the outside, and the ship took off, rocketing out of the atmosphere.

The Normandy narrowly evaded the flaming chunks of destroyed ships, and jumped into FTL, leaving Earth behind...


	31. Priority: Mars

_It was only a few moments after the Fall of Earth that Commander Shepard was redirected to the planet Mars, on Admiral Hackett's orders. More specifically, the Mars Archives, where an old colleague by the name of Liara T'Soni was searching for anything to use against the Reapers._

 _It was there that they made a discovery that would forever change how they viewed the Prothean extinction..._

* * *

The Kodiak shuttle used by the Normandy crew touched down on Mars's sandy surface.

"Still no contact from the base, but we've got a massive storm headed our way." Vega reported, sealing his suit.

"How long until it hits?" Shepard inquired, as the shuttle's door opened. Shepard, taking point, led the squad out of the shuttle, and towards the archives' entrance.

"Half hour, tops." Vega answered. "After that, we're going to have trouble keeping up comms with the Normandy."

"Understood." Shepard replied, jumping off a short cliff.

"What's that?" Vega asked, looking at a corpse leaned against a power relay.

"Alliance, Sergeant Reeves." Kaidan answered, examining the dog tags. "Looks like he didn't put up much of a fight."

"Just what the hell is going on here?" Vega wondered.

"No idea." Shepard responded. "But we should keep a low profile until we know what's going on."

The team turned a corner, and saw multiple vehicles, all bearing the markings of Cerberus. Shepard gave the order for them to take cover, and observed the Cerberus Troops' movements.

One soldier, clearly the leader, approached a researcher that was on his knees. The soldier pressed a pistol to the researcher's head, and mercilessly pulled the trigger.

"Holy shit!" Vega breathed. "They're executing them!"

"Weapons free!" Shepard ordered, popping out of cover to open fire. She hit the leader in the back of his head, killing him, and causing the rest of the troops to scatter.

"They know we're here now!" Vega yelled, throwing a grenade at another trooper.

Kaidan let out a biotic blast, which hit a trooper, causing him to be thrown over the edge of a cliff, down into the deep crater under the archives, where he would surely meet his end.

Only two troops remained, which were swiftly taken out by gunfire. With the immediate threat taken care of, the team pushed forward, walking past three troop transports.

"Doesn't look like they came in force." Vega remarked, as they all stepped into the cargo lift.

"Yeah." Shepard agreed. "Just a few trucks."

"They must've had someone on the inside." Kaidan hypothesized. "No way they could take this facility with anything less than a full battalion."

Shepard walked over to the lift's controls, and pressed the activator. The massive blast door sealed, and the lift filled with oxygen, allowing the team to remove their helmets. Soon after, the lift started moving up.

The lift stopped at a small garage, which was empty, save for a few vehicles. The team stepped off, and began walking forward, only to dive into cover once they heard loud banging coming from the ventilation ducts.

Shepard kept peeking out, her eyes trained on the duct, and her weapon ready. The duct's cover popped off, and fell to the ground, allowing an Asari to jump down to the floor. An Asari that Shepard could place anywhere.

Liara turned around, and threw a singularity at the Cerberus Troopers that had jumped down after her. The troopers floated upwards, and lost their weapons, allowing Liara to easily pick them off.

Shepard smiled, and started walking towards Liara. "Easy, Lieutenant." Shepard said, pushing Vega's gun down. "She's with us."

"Shepard!" Liara turned around. "Thank the goddess you're alive!"

"You know me." Shepard smiled. "It takes more than a few Reapers to put me down."

Liara snorted, but her smile fell. "I was so worried when the reports came in... I'm sorry about Earth."

"Yeah." Kaidan butted in, stepping forward. "It was... hard to leave."

"Kaidan. I'm sorry. But... why are you all here?"

"Hackett ordered us." Shepard answered. "Hackett said you found something in the Archives."

"Oh... _that."_ Liara grimaced. "Approximately one week ago, I found a series of logs made by a team of Prothean researchers while they were here. They were in the process of studying humanity's development while the Reapers attacked."

"While the Reapers attacked?" Shepard repeated. "Why?"

Liara shook her head. "I don't know. Prothean data storage is advanced, but it's not infallible. Most of the logs were heavily corrupted. Save for a few logs leading up to the final one."

"Okay. So, what was in these logs."

Liara rubbed her forehead. "Shepard, I don't know how to explain this, but the Protheans... They _let_ the Reapers harvest them!"

"They were indoctrinated?"

Liara shook her head. "No. The logs that survived showed that everything about the researchers' behavior was normal."

"So, what happened?" Shepard inquired.

"The Protheans learned... something. According to the logs, the Reapers across the galaxy all sent out data transmissions to every terminal capable of receiving them. From what the Protheans were able to gather, some sort of cataclysm would happen very soon, relatively speaking, on a _universal_ scale. And the only hope they had of survival, was to submit to the Reapers."

"A cataclysm?" Kaidan repeated. "So the Reapers are killing everybody, so everybody won't die?"

"The logs don't say for certain." Liara responded. "The only concrete data about the cataclysm that survived, was that they referred to it as 'The Silence.' But the name is hardly an indication of what it actually is. It could be any number of things. A universe-wide extinction event, some kind of mass destruction, or something worse than the Reapers..."

"Worse?" Vega repeated. "What could be worse than the Reapers?"

"The Reapers only limit themselves to our galaxy. So, why haven't we heard from any species in _other_ galaxies? The only thing any of our species has received when trying to detect extragalactic transmissions, was _silence_." Liara finished. "So if the Reapers aren't responsible... who is?"

Shepard shuddered. "That's a... _scary_ thought."

"Of course, that's simply conjecture. For all we know, there could be some sort of undiscovered natural phenomenon that prevents extragalactic transmissions from entering our galaxy. This... 'Silence' could occur in a few eons, or in a few years. There's simply no way of being certain."

"One thing _is_ for certain, though." Shepard began. "We _need_ to stop the Reapers. Is there anything in the archives that can help us with that?"

Liara shrugged. "I don't know. So far, the only data I've obtained was in the logs, which are irrecoverable at this point. But the archives has zettabytes of data that still haven't been researched. There could be something in there... If Cerberus hasn't gotten to them first."

"So it's a race to the archives." James stated.

The room suddenly shook, and a door at the far end of the garage sparked as Cerberus cut their way through.

"We've got company!" Shepard pointed, moving into position.

"Bring it on." Vega grunted, readying his gun.

"Not this time, Lieutenant." Shepard turned around. "Get back to the shuttle. If this goes south, I want the option for a quick extraction.

Vega clearly wasn't pleased with her orders, but complied anyway. "Aye, aye." James ran over to the lift, and took it down, the blast door sealing behind him.

"Here they come!" Kaidan yelled, as the door that was being cut finally gave away.

Shepard got back into cover, and opened fire. But, the Cerberus troops had the advantage of high ground, and used it to their advantage. They hit behind the metal railing, using the railing as effective cover. With the option of simply unloading all their shots into them gone, Liara threw out another singularity, causing the troops to float up, and over the railing. Once they were free of the singularity's bubble, they fell all the way to ground level, where they were made easy targets for the team.

With the Cerberus troops in the immediate area dispatched, the team pushed forward, into the archives.

* * *

As the team pushed to the Prothean Archives itself, they mopped up any Cerberus resistance they came across. Along the way, they discovered that one of the researchers, one Doctor Eva Core, was the Cerberus agent that gave Cerberus access to the facility. More disturbing, they discovered that the Cerberus troops had been modified with Reaper tech, turning them into something resembling husks in appearance. The three continued pushing ahead, going across the tram line leading to the archives. They destroyed the last bit of Cerberus guarding the entrance, and proceeded inside.

The Archives themselves was definitively Prothean, similar in appearance to the beacons scattered across the galaxy. The Archives had several lines of circuitry running all across the outside, pulsing blue with the contained knowledge of a species long dead.

"Kaidan," Shepard addressed, "See if there's any Cerberus personnel still left inside."

Alenko nodded, and stayed back near the entrance, beginning a counter-clockwise sweep of the room.

Shepard and Liara, walked over to three terminals in front of the Archives themselves. As soon as they began trying to access the data, a holographic projection behind them flickered to life, displaying a man in a clean suit, holding a cigarette.

 _"Shepard."_ The Illusive Man addressed, his hologram flickering with instablity. The sudden appearance of TIM caused Liara to startle, and whirl around faster than any quick-draw, leveling her pistol at the hologram.

"Illusive Man?" Liara frowned. Seeing that there was nothing her pistol could do to the hologram, she holstered it, and stood next to Shepard, glaring holes into the Illusive Man.

 _"Fascinating race, the Protheans."_ He began, looking at the Archives with appreciation. _"They left all of this for us to discover, but we've squandered it. The Alliance has known about the Archives for more than thirty years, but what have they done with it?"_

"What do you want?" Shepard demanded.

 _"What I've always wanted."_ TIM answered. _"The data in the Archives holds the means to our understanding of, and eventually the solution to, the Reaper threat."_

"I've seen your 'solution.' You're people are turning into monsters." Shepard argued.

 _"Hardly."_ TIM fired right back. _"They're being improved."_

"Improved!?"

 _"That's what separates us, Shepard. Where you see the need to destroy, I see a way to control. A way to dominate and harness the Reapers' power. Imagine what could be done for humanity if_ we _controlled_ them."

"Earth is burning, and you're hatching a scheme to control the very things causing the problem!?" Shepard demanded.

 _"You've always been shortsighted. Hasty."_ The Illusive Man argued, shaking his head. _"_ _Something worse is coming, the Protheans learned that themselves. And only the Reapers have the means to stop it. Refusing to control the Reapers, instead trying to destroy them, is a foolhardy course of action."_

"Refusing to destroy them s 'foolhardy!'" Shepard retorted.

The Illusive Man took a drag from his cigarette, and pointed at Shepard. _"This isn't your fight any longer. You can't defeat the Reapers."_

"Then work with me! Give me control of your resources, and I'll stop them!"

The Illusive Man merely shook his head. _"That's no longer possible Shepard. You know as well as I do that any alliance made between us will be temporary at best. More importantly, I don't want the Reapers destroyed. If we can control them, we can bring humanity to the apex of evolution, and beyond."_

"Haven't you learned anything!? You can't control the Reapers! People better than you have tried, and they're all dead, or indoctrinated."

 _"I don't expect you to understand, Shepard. And I'm certainly not looking for your approval. You were a tool, an agent with a singular purpose. And despite our differences, you were relatively successful. But like the rest of the relics in this place, your time is over."_

"Enough talk. Liara!"

Liara simply nodded, and moved to start the data transfer.

 _"Don't interfere with my plans, Shepard."_ TIM threatened. _"I won't warn you again."_

Shepard scowled. "Duly noted."

"Shepard!" Liara cried, grabbing the Commander's attention.

"What?" Shepard asked, walking over to the Asari. The Illusive Man sinsterly smiled, and vanished.

"The data, it's not here!" She said, frantically typing commands into a console. "It's being erased!"

"Damn it!" Shepard cursed. "How's he doing it!?"

"It's local." Liara answered. "And the files are not being deleted, they're being uploaded."

"Hey! Step away from the console." Kaidan barked at someone from across the room. Kaidan was kicked to the floor, and soon after, the Archives went off-line.

Dr Core sprinted out of the small room, and across the chamber.

"After her!" Shepard hollered, taking off in pursuit, with Kaidan and Liara not far behind.

"She's faster than she looks!" Liara shouted.

Core lured them to the security checkpoint, and shut the doors behind them. Shepard overrode the door controls, only for an incineration blast to be fired at her once they opened. Core then _jumped_ into an open panel in the ceiling, and dropped down on the other side of the checkpoint.

Shepard overrode the lockdown, allowing the shutters to open, and the team continued their pursuit. Core sprinted through an open door on the left of the room, and up a ladder, onto the base's roof.

The team climbed up after her, and Shepard opened a comm link. "James? You read me?" She asked, as they chased Core through the base's supports. The Commander's only response was broken static. Hoping that Vega's end was clear enough to make her out, Shepard continued. "Cerberus has the data! Radio the Normandy, get them down her now!"

They climbed up another ladder, as Core sent out more incineration blasts. A Cerberus shuttle descended from the skies, and held at the end of the walkway, its hatch wide open so that Core could jump inside.

"She's getting away!" Shepard yelled, firing her gun. "Damn it!" She cursed, watching the shuttle's hatch close. "James? Normandy? _Anybody!?"_

 _"I got this one!"_ Vega radioed, the Alliance shuttle suddenly breaking through the storm.

Vega gunned it, and proceeded to ram the Cerberus shuttle at full speed. The Cerberus shuttle's fuel lines broke, and the shuttle burst into flames, its metal carcass dropping to the floor like a brick. Vega's shuttle crashed as well, though he was largely more intact, and he stepped out safely.

Vega rolled his shoulders, and cracked his neck. "Normandy's on-route." He notified, shaking off the whiplash. "They'll be here soon."

The Cerberus shuttle's door abruptly began banging, and flew off of the chassis, falling against the ground.

Inside the shuttle, the flaming mech body of Dr Eva stood to full height. Kaidan, not wasting any time, drew his pistol, and began firing.

Core sprinted forward, shrugging of each of Kaidan's shots, and picked him up by the neck, slamming him against the shuttle.

She pressed two of her fingers to her metal temples, clearly contacting someone. "Orders?" She waited for a moment, and upon receiving them, began bashing Kaidan against the shuttle. Over and over again. It was only when Shepard began firing at her did Core stop.

The mech turned around, and began sprinting forward. In that moment, everything seemed to move in bullet-time for Shepard.

The Commander fired every shot her thermal clip allowed her to. With one final shot to the mech's shoulder, Dr Eva fell over, sparking.

"Grab that thing!" The Commander ordered, pointing at the mech, as she ran over to pick up Kaidan.

 _"Commander, we've got Reaper signatures in orbit!"_ Joker radioed, as the Normandy descended towards the base. The shuttle bay door opened again, allowing the team to run up inside, Vega and Shepard holding the limp forms of Dr Eva and Kaidan, respectively.

The door closed once more as the Normandy began taking off, and as the Reapers began descending upon Mars, signaling that the Sol System was now completely lost to the Reapers.

* * *

Shepard ran into the medical bay, with Vega and Liara in tow. She gently set Kaidan down on one of the beds, while Vega unceremoniously did so with the mech.

"Kaian needs medical attention." Liara stated, looking Shepard right in the eyes. "We have to leave the Sol System."

Shepard sadly looked down. "I know."

"We need to go to the Citadel, we can find help there." Liara finished.

Shepard nodded. "Set a course for the Citadel, Joker."

 _"Roger that."_ The helmsman responded.

Shepard looked over to the mech with disdain. "See what you and EDI can learn from that... _thing."_

Liara nodded, and walked over to the mech, setting to work.

 _"Commander."_ EDI suddenly addressed. _"I am receiving a signal over the secondary QEC. I believe it is Admiral Hackett."_

"Patch it through, EDI." Shepard ordered, moving to exit the medical bay. But once the door opened, she could see someone standing in her way.

The Doctor stepped forward. "Belay that order, EDI." He told the AI, causing the Commander to frown. "Shepard, you and I need to talk."


	32. Priority: The Citadel I

"Sorry about the interruption, Shepard, but it's important." The Doctor semi-apologized, following Shepard to somewhere they could talk privately. "How are Susan and River treating you?"

"They're good." Shepard answered. "They've been helping with the Normandy retrofits. They're probably down in Engineering right now, if you want to see them."

The Doctor shook his head, and followed Shepard into the sound-proofed conference room on deck two, just outside the war room. "I would, but this is more important." He took a small, flash-drive like device out of his pocket, and connected it to his omni-tool... somehow. Upon connection, a hologram of what appeared to be a ship of some kind was projected, along with Galifreyan glyphs.

"What is it?" Shepard inquired.

"A weapon." The Doctor answered. "Capable of destroying the Reapers in one shot."

"Where did you find this?"

"On the planet Edom, in the Large Magellanic Cloud." The Doctor answered. "It's where the Reapers retreat to in between their harvests. On the planet, I found a Time Lord scientific outpost, and these plans were inside. I think the Time Lords, a very long time ago, studied the Reapers, and came up with this to use against them."

"And you're certain we can use it against the Reapers?"

The Doctor nodded. "Absolutely."

Shepard, however, frowned. "If it's capable of destroying the Reapers, then how come the Reapers are still around? Wouldn't the Time Lords have used it?"

"They would have, but this thing," He gestured to the plans, "Is filled to the brim with all sorts of tech, designed to breach the Time Vortex, act as a signal hijacker, and a massive energy weapon, all in one. The problem is, the designers needed a massive transmitter if they wanted the pulse this thing would make to cover the entire galaxy."

"So, without this transmitter, they couldn't fire it?"

"Precisely." The Doctor confirmed. "The builders of this thing called it 'The Catalyst.' It appears to have been some sort of previously built structure, given that this thing is designed to latch on to it."

"So unless we find it, this thing is little more than a glorified paperweight?"

"Yes. Unfortunately, I can't just go back in time to figure out what it was. The TARDIS had enough trouble getting to Edom as it were."

"Trouble?" Shepard's eyebrows raised.

"She... doesn't react well to Reaper technology. Now listen, this thing is big, _but_ it's well within the engineering capabilities of the galaxy's civilizations. As long as you have enough time, any of the galaxy's civilizations could build it on their own."

"Time isn't something we have a lot of, right now."

"Well then, we can go to the Citadel, and get the Councilors to spare some manpower to pour into this thing!" The Doctor retorted.

Shepard sighed. "Send a copy of the plans to my omni-tool, and I'll give them to Hackett. I can't guarantee anything from the Council, though. Lately they haven't been too... receptive to Time Lords."

The Doctor raised his eyebrows. "What does that mean?"

"It means they think the Time Lords are coming back to wage a war, and the Council's scared shitless so they've set standing orders to execute any Time Lord or their agents on-sight."

"That's... not pleasant."

"No. But now that the Reapers are here, hopefully, they'll realize that we have bigger problems."

"Indeed."

"Now, if you'll excuse me, I've got an urgent call from Admiral Hackett that I need to answer. We're going to be arriving at the Citadel in a few hours, so get something to take to the Council prepared, got it?"

"Right." The Doctor nodded.

With that, Shepard left to go speak with Hackett.

* * *

A few hours later, the Normandy dropped out of FTL, and approached the Citadel. The ship plunged into the Citadel's atmosphere, and approached the Presidium ring. The Normandy proceeded into Docking Bay D24, and the docking clamps latched on, holding the Normandy in place as the docking tube attached to the airlock, allowing the crew to depart.

The door into the Docking Bay's lounge area opened up, and a team of doctors wheeled Kaidan out of the Normandy.

"Barely got a pulse here!" One reported to another.

"Move 'em out!" The Turian at the front ordered, he and the rest of the group taking a right, proceeding to the elevator.

"Where are you taking him?" Shepard inquired.

"Huerta Memorial." The Turian answered. "Finest care on the Citadel."

Shepard nodded, and stopped.

"We're not going with?" Vega asked.

The Doctor shook his head. "Shepard and I need to speak with the Council." The Time Lord explained.

"Right." Vega looked towards the entrance to the docks, and noticed C-Sec's Captain Bailey approaching. "Looks like they're coming to see you."

Shepard turned around to face the man. "Captain Bailey." She shook the man's hand. "Good to see you again."

"You too, Shepard. Though, it's 'Commander' Bailey now."

"...Sorry?"

Bailey chuckled. "Thanks. Now half my job is escorting dignitaries and dealing with political bullshit... No offense."

"Heh. None taken." She assured. "So, you're here to take us to the Council?"

"I'm here to tell you that the Council's expecting you, but their busy dealing with their own... know, with the war and all." Bailey led them to the scanners, and stopped. "They apologize for the inconvenience, and blah, blah, blah... Meet them here, at Udina's office." Bailey sent a nav point to Shepard's omni-tool. "They'll be ready soon enough."

"All right." Shepard nodded.

"You might have time to go by the hospital, if you want to see your friend."

"Thanks. I might go do just that."

"You go on ahead." The Doctor told Shepard. "I'll go up to Udina's office."

"One of my men can show you the way." Bailey told the Time Lord. The Doctor nodded, and followed a C-Sec officer into the elevator. "You?" Bailey asked Vega.

"Nah." The Marine shook his head. "I'm just a tourist today. I'll try not to get into trouble." He finished, walking off.

Bailey suddenly pressed a finger to his ear, receiving a status update from one of his officers. He sighed, and shook his head. "The other half of my job." He explained, walking away, leaving Shepard to her own devices.

* * *

Shepard stopped by Huerta memorial, and checked on Kaidan's status. Apparently, the damage was a lot worse than it looked. According to the doctors, several ribs were broken, his spine was fractured in several places, and his brain had swelled up, cutting off blood flow. It was a miracle he'd survived long enough to get treatment at all. The doctors had managed to stabilize his condition, but he wouldn't wake up for several days, at least. The doctors returned to operating on Kaidan, and so Shepard was forced to leave. On her way out of the hospital, she ran into Doctor Chakwas, and convinced her to come back to the Normandy.

Now that her business in the hospital was done, Shepard proceeded to Udina's office. Inside, his Asari assistant informed Shepard that Udina and the Doctor had already gone up to the Council Chambers, and were waiting for Shepard to arrive. So, Shepard allowed the assistant to lead her up.

"We've got our own problems, Councilor." Shepard could hear the Turian Councilor say to Udina. "Earth is not in this alone."

"But Earth was the first Council world hit." Udina retorted. "By all reports, it faces the brunt of the attack."

"By _your_ reports." The Salarian Councilor corrected.

The Doctor was standing on the edge of the platform in front of the Councilors, shaking his head. Shepard walked up to stand next to him, and looked up at the Councilors.

"The reports are accurate." Shepard told them. "Earth _was_ attacked... by the Reapers. And it's just the beginning. We need your help. Everything you can spare."

"Each of us faces a similar situation." The Asari Councilor spoke up. "Even now, the Reapers are pressing on our borders. And that's saying _nothing_ of the Time Lords."

"For the last time, the Time Lords aren't trying to go to war with you!" The Doctor yelled.

The Asari Councilor ignored him. "If we lend you our strength to help Earth, our own words will fall."

"That may be true, but this isn't an enemy we can defeat on our own!" Udina retorted.

"And so we should just follow you to Earth?" The Salarian Councilor asked.

The Turian Councilor gestured for the others to calm down, then asked Shepard: "Even if we united our fleets, do you _really_ believe they could defeat the Reapers?"

"I don't expect you to follow me without a plan." Shepard said. She nodded to the Doctor, causing the Time Lord to bring up his omni-tool, projecting the holographic plans for the Anti-Reaper Weapon.

"Councilors," The Doctor began, "these plans were devised after centuries of research on the Reapers by the Time Lords. If you all combined your resources, it could be built in only a few months."

"Plans for what?" The Turian Councilor skeptically inquired.

"A weapon." The Doctor answered. "The original designers called it 'The Moment.'"

"And it is capable of destroying the Reapers?" The Salarian Councilor asked.

"I believe so."

"The scale is... It would be a colossal undertaking." The Salarian Councilor stated.

"Yes." The Doctor nodded. "But like I said before, if you all pooled together your resources, then it could be built within only a few months."

The Asari Councilor narrowed her eyes. "How do we know that this isn't a trap, Time Lord?"

"Councilor, my people have technologies that your people haven't even dreamt up in fiction yet." The Doctor told her. "If we really wanted you all dead, we wouldn't be speaking to you now."

The Asari Councilor continued frowning. "If the Time Lords had the capacity to destroy the Reapers, then why are they still around, hmm?"

"There was a missing piece. The 'Catalyst.'" The Doctor answered. "This thing," He gestured to the plans, "is nothing more than a really big battery. The Time Lords could've deployed it right then and there, but without a transmitter large enough, the blast wouldn't have been enough to cover the entire galaxy."

"Do you really believe this will work?" The Turian Councilor inquired of Shepard.

"The Doctor's the only expert on Time Lord technology we have." Shepard stated. "If he thinks it'll work, then so do I. And while I haven't always agreed with him, Udina's right. This isn't an enemy no one species can defeat on their own."

"The Time Lords." The Doctor coughed.

Shepard glared at the Doctor for a moment, and then turned back to the Council. "The Reapers won't stop at Earth. They'll destroy _everything_ if we don't stop them."

"The cruel and unfortunate truth is that while the Reapers focus on Earth, we have time to prepare and regroup." The Asari Councilor said, before the other Councilors could get words in edgewise.

The Salarian Councilor narrowed his eyes at the Asari Councilor, but his expression quickly returned to normal as he began speaking to Shepard. "We are convening a summit amongst our species. If we can secure our borders, we can give you our full support."

"I'm sorry, Commander." The Asari Councilor apologized, though her tone made it clear that she wasn't sorry at all. "This is the best we can do." She finished. With that final statement, she and the other Councilors left.

Udina lingered for just a few seconds, long enough to say something. "Shepard, meet me in my office." He ordered, departing as well.

The Doctor looked at the gradually shrinking form of the Asari Councilor, his eyes narrowed and brow furrowed in suspicion. "At least they're not totally denying us support. I'll do what I can to learn more about this thing, but in the meantime, I have a few... things I need to take care of."

Shepard nodded, and departed the Council chambers, heading back down to Udina's office.

* * *

"They're a bunch of self-concerned jackasses, Shepard!" Udina furiously ranted once he crossed the doors into his office.

Shepard was stood up, and watching Udina angrily gesticulate with fury at their current situation.

"We may have a seat on the Council, but humanity will always be considered second-rate!" Udina continued.

"It seemed to me like Sparatus and Valern wanted to help, but Tevos wouldn't let them do anything." Shepard shook her head.

"That is _exactly_ what happened." The Turian Councilor spoke up, suddenly entering.

"Councilor." Udina greeted.

"Commander," Sparatus addressed, ignoring Udina for the moment, "I can't give you what you need. But, I _can_ tell you how to get it."

"I'm listening."

"Primarch Fedorian called the War Summit." Sparatus explained, pacing around Udina's office. "Unfortunately for us, we lost contact with him shortly after the Reapers hit Palaven. Those meetings won't proceed without him. The Normandy is one of the few ships that can extract him undetected."

"As much as I'd like to help out, so far you've only told me how this benefits _you."_ Shepard crossed her arms.

" _I_ can't help you directly." Sparatus outlined. "But the _Primarch_ can _._ He can give you access to ships, troops, and resources that I can't authorize you to use otherwise. Trust me, a Primarch that owes a favor is a powerful ally, indeed."

"We're at war, and I'm supposed to play _politician?_ " Shepard snorted.

"If it gets you what you need, what does it matter?" Sparatus retorted. He walked over to a vid screen on the wall, and pulled up an intelligence report. "Our latest intel says that the Primarch was moved to a high-security installation on Palaven's largest moon, Menae. I've done all I can to help, the rest is up to you." He moved to walk out, but stopped before he could cross the door's threshold. "Oh, there is one other thing. We've decided to uphold your Spectre status." He told Shepard, tapping a few commands into his omni-tool. "And various resources will be made available to you. Good day." He bid, leaving Udina's office.

"Well, that went well." Shepard stated, once the door shut.

"It's a start." Udina conceded, sitting back down at his desk. "In the meantime, I'll talk to the others, see if we can support this summit. Move things along."

"Thanks." Shepard nodded, and she left Udina's office, now on a new mission.

On her way back to the Normandy, Shepard stopped by the Spectre office, and used the terminal inside. She read through most of the entries, though the one that caught her attention was pertaining to Engineers Donnelly and Daniels. She authorized their release, purchased some new gear with the left over credits in her bank account, and proceeded back to the Docking Bay D24.

Shepard crossed the airlock, and boarded the ship. Once everybody reported in that they were on board, and at their stations, she gave the order for immediate departure.

The Normandy's engines powered up, and the docking clamps attacked to the ship released, allowing the ship to back out of its berth. The Normandy turned around, and the engines flared up to full power. The Normandy darted away like a speeding bullet, and left the Citadel's atmosphere, heading back out into the inky blackness of space.


	33. Interlude: The Normandy I

The smell of smoke filled Shepard's nostrils, and the Commander confusedly looked around, trying to get a handle on where she was. She was in a forest, or rather, it used to be a forest. The dead husks of alien trees surrounded her, and silver leaves piled on the ground. Shepard looked down, she was in her N7 armor, but she didn't remember putting it on.

For that matter, she didn't remember how she got here either.

Shepard looked up, trying to see if there were any aircraft passing by.

Only silence was the response.

Suddenly, one of the leaves cracked under someone's step.

Shepard turned around, trying to see the culprit. A person, in white and pink armor, ran away, deeper into the forest. Not thinking, Shepard gave pursuit.

Blades of red grass were flattened by Shepard's feet, as she ran to catch the other person.

 _"Shepard..."_ A ghostly voice called out, barely audible.

Shepard ran in between two trees, trying to keep up with the person.

 _"Shepard..."_ The same voice whispered.

The person stopped, and Shepard closed the distance. The person finally turned around, allowing Shepard to recognize the person.

 _"Shepard..."_ Ashley Williams whispered. Her skin was pale, deathly white, and her eyes were entirely white. A second later, a flash of red light illuminated where the two were standing, and a fire broke out.

The fire crept across Ashley's skin, burning away her hair, and charring her flesh. Her flesh entirely burned away, leaving only Ash's charred skeleton. The skeleton then blew away, like dust in the wind.

All of it happening while Shepard was reaching out, trying to grab her friend's hand, and save her.

But she failed. And Ash paid for it.

* * *

Shepard's eyes snapped open, and Shepard took in a sharp breath, sitting up quickly. She was back in her cabin on the Normandy, and calmed down once she realized the events that had just transpired were all just a dream.

The door chime rang, prompting Shepard to get up from her bed, and answer it.

The door opened, and the Doctor was on the other side, waiting.

"Doctor," Shepard greeted, "Is there something you need?"

"I've been forwarding information on the Moment to the Turian Councilor." The Doctor answered. "The amount of manpower and resources it needs, stuff like that... He says he can spare the help, but he won't until the Primarch is safe and sound. We _need_ to get that Primarch rescued, and soon."

Shepard sighed. "I know. Can't we just use the TARDIS?"

The Doctor shook his head. "Like I said before, she doesn't react well to Reaper technology, and with all the Reapers around... To be honest, I really don't know what'll happen." He explained.

"Well damn."

"You okay?"

"Yeah, it's just..." Shepard sighed. "There were a lot of people back on Earth. I could hear them, screaming and crying in the streets as the Reapers attacked. It was... hard leaving them behind."

"That's good." The Doctor responded. At Shepard's piercing look, he continued. "Not the people screaming and crying, but it being hard to leave them behind. Don't let it get easy, because once it is, you're no better than the Reapers."

"Right." Shepard nodded.

Abruptly, the elevator door opened, and a woman stepped out. "Commander Shepard?" The woman addressed. "I'm Specialist Traynor-oh." She stopped, once she noticed the Doctor's presence. "I beg your pardon. I thought you were on your own."

"Don't worry about it." The Doctor waved off, walking back into the elevator. "I'm just leaving. When you're done, Shepard, meet me in Starboard Observation."

Shepard nodded, and turned to Traynor. "You were saying?"

Traynor nodded, and snapped a salute. "I'm Comm Specialist Samantha Traynor, Alliance R&D. I was part of the team retrofitting the Normandy after you turned it over to the Alliance."

"Right, the retrofits." Shepard remembered. "Why don't you tell me about those?"

"The ship's now in line with Alliance regulations, and it has new top-of-the-line Quantum Entanglement Communicators." Traynor outlined. "The ship is mostly the same as it was before, save for deck two. The Science Lab has been replaced with the meeting room, and the Armory has been moved down to the shuttle bay to make space for the War Room. Oh, and Doctor T'Soni has set up in the old XO office on deck three. The weapon systems have also been upgraded with technology from the Torchwood Archives. So, the Normandy's still the same ship as before, just a little bit upgraded, and flying Alliance colors now. Speaking of which, Admiral Hackett would like to speak with you at the Vid-Comm."

Shepard nodded. "Thank you, Specialist. You're dismissed."

Traynor nodded, snapped off a salute, and proceeded back to her post on deck two.

Shepard lingered in her cabin for a moment, checking her private terminal. So far, there wasn't anything too important, save for intel about a Cerberus base on Sanctum, and a priority mission to Eden Prime. Archiving the messages, she moved to exit her cabin, before the sound of something scampering across the floor grabbed her attention.

She turned around, and tried to find the source of the sound.

Following the source of the quiet pitter-patter, Shepard came to a tiny vent, and crouched down to it, she looked inside, and her day brightened ten-fold.

"Boo!" She happily cooed, reaching into the vent. She grabbed the tiny Space Hamster gently, and pulled it out. "Mama's missed you!"

"*Squeak!*" Boo squeaked, trying to crawl out of Shepard's hand, and into his cage.

"Aww, did the mean old Alliance people not feed you? There." She gently set him down in his cage. The hamster crawled over to the food bowl, and immediately began eating up.

Then, she proceeded down to deck two.

Stepping out of the elevator, she immediately went right, into the war room. She passed through the scanners, walked past the meeting room, and into the war room proper.

Shepard walked into the comm room, stood in front of the QEC, and turned it on.

 _"Commander,"_ Hackett greeted, flickering into existence, _"Udina's updated me on your meeting with the Council. Sounds like they're running scared."_

"We did present them with a lot of unknowns." Shepard was willing to give them that. "They wanted immediate solutions, not theory and blind leaps of faith. And Tevos was so concerned about a possible Time Lord attack that she wouldn't let the others get a word in edgewise."

Hackett shook his head. _"Theories are all we've got right now. What's your plan?"_

Shepard sighed. "Right now, my immediate goal is getting the Turian Primarch off Menae so the war summit he's called can go smoothly. if the war summit goes well, I can bypass the Council and get help directly from their leadership. After that, I'm thinking I can head to Gallifrey, and see if I can get the Time Lords to help."

 _"That's good."_ Hackett nodded. _"This is where we can start laying the ground for our counter-attack."_

"It isn't much so far."

 _"Then do something about it. Build alliances, get everybody and everything you can to help the cause."_

"What about the Moment?"

 _"Find me people who can help build it. And if you can't, I'll take anything. Ships, people, resources... But the most important thing is this: Buy us time to figure out the device. The Moment is useless if the Reapers can find it and destroy it while it's still under construction."_

"The Doctor's still working on deciphering the schematics himself."

 _"Then when he gets done, have him send me the relevant data. Then, we pool_ everything _we can to get it completed. After that, we deploy it. But without knowing exactly how it operates, we're risking the biggest backfire in history. That's why we need the plans figured out, to know we're not kids playing with a loaded gun."_

"Understood, sir." Shepard nodded.

 _"Then make it happen, Commander. Until then, I'll be expecting regular updates on your progress. Hackett out."_ He finished, and the hologram flickered and vanished.

Shepard sighed, and left the war room, heading down to deck three. She hoped the Doctor made some progress.

* * *

Shepard walked into Starboard Observation, the door sealing shut behind her. The TARDIS was parked in the corner, and various bits of scrap and junk were scattered across the floor.

The Doctor was in the middle of the room, fiddling with what looked like a satellite dish made out of the junk on the floor. "Hello, Shepard."

"Doctor." The Commander returned. "What are you doing?"

"I'm _trying,"_ He grunted, pushing a bit of metal into a slot, "To send a message to the Time Lords. Normally, I'd use a psychic container, but with all of the Reapers around, there's not a very good chance of it making it to Gallifrey."

"Why send a message?" Shepard asked. "Why not just go to Gallifrey and ask for their help directly."

"You know how I said the TARDIS doesn't react well to Reapers? Well, take a look inside."

Shepard raised an eyebrow, and peeked inside the TARDIS. The inside was completely dark, devoid of light and totally silent.

"So, you're stranded with us for the time being? No crazy adventures while the rest of us are in the middle of a warzone?"

"It seems that way, yes." The Doctor responded, still focused on the dish. He sighed, and shook his head. "I had no idea the Reapers were so powerful. Powerful enough to strand a TARDIS in one place and time, at least. Whoever created them must have known a lot about TARDIS technology."

"How _did_ the TARDIS get like that?" Shepard questioned.

"If you'll recall I showed up on the Normandy while you lot were still leaving Mars. All those Reapers in close proximity to the ship must be what caused the TARDIS to break down. She should be fine in a few hours, though."

"Good to know." Shepard nodded. Shepard shifted her weight, and asked the next question that came to her. "What'd you find in the LMC? Other than the plans for the Moment?"

"I found a lot of Reaper space stations." The Doctor answered, attaching a power cable to the transmitter. "Whoever built the Reapers originally had a pretty sizable presence. But other than that and the plans, nothing."

"Speaking of the plans, Admiral Hackett's trying to get them figured out." Shepard said. "Trying to figure out how to work the Moment."

The Doctor snorted. "It'll take your best scientists at least a few hundred years to find the light-switch. But don't worry, I'm working on them." He gestured over to a nearby hologram of the plans, projected over a desk. Strange symbols were projected alongside the plans, with more recognizable Gallifreyan symbols on the bottom. "The overview of the plans are in an extinct form of Old High Gallifreyan, so obscure that I don't know it. I've got the Sonic Screwdriver running a translation program, but without the TARDIS's Index Files, it's going to be a while before they make sense."

"That's good. When they're done, send them to Hackett." Shepard ordered. "Do you need anything for your project?"

The Doctor shook his head. "I don't think so, but Susan said she wanted to speak with you. She's down in Engineering, if you want to go talk to her."

"Then I'll go do that." Shepard nodded, leaving the room. Before she headed down to Engineering, she decided to see what Liara was doing.

Shepard touched the control panel, and the door slid open, allowing Shepard entry.

Dozens of screens lined the wall, showing a map of the galaxy, with yellow lines across it. Large server banks were across from the screens, humming and glowing with power.

"Commander Shepard!" A blue holographic orb greeted, coming out from behind the servers. Two spinning half-spheres surrounded the central sphere, and a blue eye-like circle was on the front. "It's a pleasure to see you again!"

"Hey, you're the drone from the Shadow Broker's ship." Shepard recognized.

"That is correct, though Doctor T'Soni now refers to me as 'Glyph' instead of 'Info Drone' ninety-five percent of the time." The little VI responded. "If you have a moment, I'd like to draw your attention to this terminal." He floated over to a terminal next to the computer banks. "It analyzes information packets." Glyph explained, as a display flickered into existence. "If you find any useful data, I can research upgrades for you."

"That's useful." Shepard said. "Have you found anything useful already?"

"I have." Glyph tilted forward in an imitation of a nod. "Modified shield systems, based off data given to us by the Doctor, are now available for installation in the Normandy. According to the simulations, the new systems will be able to absorb 1.21 terawatts of energy before collapsing."

"Great Scott..." Shepard responded.

"...Indeed." Glyph humorlessly replied. "Should you come across relevant data packets, I will inform you. In the meantime, Doctor T'Soni would like to speak with you. Have a pleasant day!"

Once the VI was done with his little spiel, Shepard approached Liara. "So, I take it you've called dibs?"

"Oh, Shepard." Liara turned around from looking at her data feeds. "I'm sorry, it's just, I had a lot of equipment, and this was the most private room I could find-"

"Don't sweat it, Liara." Shepard put her hands up in a calming gesture. "How've you settle in?"

"Well enough, given the circumstances." Liara answered. Then, she let out a sigh. "Little of my data feeds survived the Reaper attack, add to that the Cerberus attack on my ship..."

"Wait, Cerberus attacked your ship?"

The Asari nodded. "I can only assume they intended to obtain control of my information network. I knew they wouldn't use it as... altruistically as I have, so I set the ship to ram into a Cerberus cruiser, after that, they both exploded. It was a magnificent display of light, I assure you."

"So," Shepard looked at the wall of screens, "What are you up to?"

"Right now, I'm trying to reorganize what little operatives I have left." Liara answered, tapping away at her datapad. "After that, the priority becomes providing aid to whoever needs it."

That gave Shepard an idea. "You know, Alliance Intelligence has discovered a Cerberus lab on Sanctum." Shepard relayed to Liara. "Do you think you have operatives that be up for going in and securing it for the Alliance?"

"Of course." Liara responded, walking over to her terminal. Seconds passed as she typed a message, and she sent it out into her network. A few minutes later, the terminal blinked as it received a response. "Done. They should have the lab secured by the time our mission on Palaven is over."

Shepard raised her eyebrows. "That was quick."

"I'm the Shadow Broker. My agents don't dawdle unless the situation calls for it." Liara explained. "Now, is there anything else you needed?"

"Actually, I wanted to know about the data we got from the archives. Have you learned anything from it?"

"Not anything useful." Liara answered. "So far, the data's only been logs and results of genetic tests on early humans. EDI and I have been trying to recover what we can, but there are still terabytes of corrupted data that we've yet to get to. If we find anything useful, I'm sure she'll let you know."

"Then I'll let you get back to work." Shepard finished.

Liara nodded, and turned back to her data feeds as Shepard left her office.

Shepard stepped into the Normandy, and went down to deck four.

* * *

Shepard walked into Engineering, and immediately, someone came darting towards her. The Commander staggered slightly as she was wrapped into a big hug.

"Grandmother!" Susan greeted.

"Susan, you're bruising me."

"Oh, sorry." Susan released the hug and stepped back. "River and I have been worried, they wouldn't let us see you while you were incarcerated."

"They wouldn't let _anyone_ see me unless it was Anderson or my security detail. Speaking of River, where is she?"

"She's in the shuttle bay." Susan explained. "She's been down there a lot lately."

"I see." Shepard nodded. "So, how have things been since I was locked up?"

"It wasn't too bad." Susan answered. "EDI managed to hack into the Alliance's network and forge credentials for us. River and I were assigned to the crew doing the retrofits so the Alliance wouldn't kick us off the ship, having nowhere to go."

"So you've both been spending the past six months as grease monkeys?"

"Well, I can't complain. The Normandy's a marvelous ship." Susan said. "Although, these uniforms are a bit itchy..."

"Tell me about it."

"The Normandy being marvelous, or the uniforms being itchy?"

"Yes." Shepard snarked. "So, have you all got everything you need?"

"I believe so." Susan nodded.

"Well then, I'll leave you to it." Shepard said, ending the conversation. Susan nodded, and got back to work, and Shepard went down to the shuttle bay.

Once she stepped out of the elevator, she heard Vega speak. At the other end of the shuttle bay, Vega and River were stood next to each other, in front of an impromptu target range.

"Ready?" The marine asked.

"As if you needed to ask." River responded.

"Draw!" Vega said. In that moment, both of their hands went to their hips, grabbing onto the pistols at their sides. They pulled the pistols off the tiny weapon docks, and put them up to aim at the targets, the pistols unfolding as they did so.

River shot first, the shot hitting the target in its exact center. Vega shot second, his shot to a little bit right of the center of the target.

Vega whistled. "Damn. That's gotta be... eight in a row?"

"I'd say it was an easy nine." River responded, twirling the gun, and putting it back on the dock. "What do you say, one more try?"

Before Vega could respond, Shepard walked over. "What is all this?" Shepard requested.

"Hey Commander." Vega greeted. "Deadeye over here was doing target practice a little while ago, and being only on the retrofit crew, I thought she didn't know how to use a gun properly, so I offered to show her the ropes. Then she just smiles, takes the gun, and fires three shots at the target while still looking at me. I looked at the target, and _all three shots_ went through the same hole! So now we have a little game going."

"Game?" The Commander repeated.

"Yeah, who can score the most bulls-eyes." Vega answered. "So far... she's been kicking my _culo."_

"At this point, he's just trying to see if he can get _one_ shot faster than me." River piped up.

"I see." Shepard nodded. "So wait, does that mean that last time you fired-"

"Eight times in a row? I did." River smiled wryly.

"How!? They don't make the triggers to be pulled that fast!"

"They don't." She winked.

"...Wow." Shepard blinked. "Think you'd be up for being on the ground team?"

"I don't see why not." River shrugged. She turned to Vega. "We'll have to finish later."

"You're on." Vega responded, walking away to go do something else.

"So, how was your time in lockup?" River asked, walking over to a workbench, and she began tinkering with her pistol.

"It wasn't all bad. I even got a decent meal once or twice. You?"

"Oh, it was terrible." River responded. "The Alliance were oh so restrictive, and Susan would not stop her incessant worrying. And I mean 'incessant' literally. She would. not. stop."

"She was just worried about her grandmother... I'm still having trouble getting used to that." She mumbled that last sentence.

"I know, but it crossed the line from 'worrying' to 'panic' a few times."

"I was there!" Cortez, the shuttle pilot, piped up. "She had to be taken up to the med-bay for a panic attack a few times!"

"I'm certain _that's_ an exaggeration, but yes, she got bad." River nodded. "She was afraid they were going to put you away for good, or outright execute you."

"I don't blame her. They had it a standing order to kill any Time Lords or their agents on-sight." Shepard sighed and shook her head. "Guess it's a good thing that the Reapers' arrival made them revoke it. What about you? What were you doing that whole time?"

"I spent most of my time tinkering with the guns away from... prying eyes. They were surprised when they found out the guns not only had better ammo capacities, but much more power as well. After they found out it was me, they gave me a reprimand for modifying the weapons without telling anyone... and then they made me Armory Chief."

"Ah, don't you just love the military?"

"Not really, no. But since I'm stuck on this ship of the damned, I'll have to make do."

"That's the most apt description of the Normandy I've heard in a while. So, have you got everything you need down here?"

River nodded. "The Alliance fully stoked the Armory. But I am working on a... secret project, and I don't have what I need to finish it."

"What kind of secret project?" Shepard asked.

"The secret kind."

"Okay... I kind of walked into that one. What do you need?"

"There are a lot of guns I need, but they're too expensive for me to buy myself, and I can't put them down as required expenses."

"Guns don't count as required expenses?"

"Normally, they would, but these are pretty special weapons. I'd have to either find them in the field, or be a Spectre to purchase them." River said. "I have the full list here." She handed Shepard a datapad. "You can find most of them in the field."

Shepard scrolled through the datapad's contents, reading off the names of each gun. "'Reaper Blackstar, Geth Spitfire, Sync Laser, M-597 Ladon... M-920 Cain!? River, these are all heavy weapons!"

River simply smiled. "Don't worry, the end result is going to be stunning. I have the Cain already -don't ask- but I still need everything else on that list."

"Then you'll get it." Shepard responded, transferring the list to her omni-tool. "Was there anything else?"

"No."

"Then I'll let you get back to it." Shepard finished. Then, the deck plating suddenly shuddered.

 _"Shepard, we are nearing Menae."_ EDI reported. _"We will arrive in thirty minutes."_

"Got it. Tell the team to assemble, we've got a Primarch to rescue."


	34. Priority: Palaven

In orbit above Palaven, hundreds of Turian ships faced off against dozens of Sovereign-class Reapers. Red beams of molten metal tore through the Turian ships, and Reaper fighters chased after the Turian fighters. Many Turian ships had already been destroyed, turning the space around Palven into an impromptu graveyard.

While the battle was occurring, the Normandy's UT-47A Kodiak flew through space, with its stealth systems engaged, on a direct course for Menae.

Inside the shuttle, the team consisting of Shepard, Liara, James, River, and the Doctor looked at the vid screens, with equal parts anger and sadness.

"Oh no. No..." Liara muttered, looking at the feed with horror. "Palaven." Blazes of fire, the size of mountain ranges, were scattered across Palaven, as massive explosions peppered the surface.

Vega raised his eyebrows, and looked at Shepard.

"We... have an old friend there." Shepard explained.

"Holy hell." Vega breathed, also looking at the screen. "They're getting decimated."

"I knew the situation was bad," River said, "but this...?"

"It'll be like this everywhere soon enough." Shepard echoed Anderson's words to her on Earth.

"Was it like this on Earth?" Liara carefully asked.

Shepard turned to her. "Yes." She stated.

"Shepard... I'm so sorry."

"Yeah."

"Commander!" Cortez piped up from the controls. "The LZ's getting swarmed!"

Shepard nodded, and stood up. "James, pop the hatch."

Vega nodded, and moved over to the hatch's controls. He pressed the button, and the hatch slid open.

Shepard drew her weapon, and instantly began opening fire on the Husks running around on the ground. Each shot tore into the back of the Husks' heads, causing them to fall instantly.

The shuttle's engines throttled down, and it touched down on Menae's Luna-like surface.

"Okay, we get in, get the Primarch, and get out." Shepard outlined. "Let's move!" She ordered, taking point. Once everyone on the shuttle stepped off, the shuttle took off, and began running aerial interference.

On the ground, the team pushed forward, bullets and sonic pulses continually flying into husks, towards the main camp.

"Hold your fire!" The team could hear a Turian soldier shout to his comrade. "Friendly inbound."

The barricade's wall lowered, allowing the team entrance into the camp. Dozens of wounded Turian soldiers lay on the ground, the medical area being too cramped to fit them in. The team stepped over the wounded, and proceeded to the prefab where the Commanding Officer was. Along the way, the team could overhear conversations telling them just how bad the situation was.

"Tebestik, get your men up on the north barricade." The General ordered his subordinate as the team approached. "Sergeant Bartus, find a way to get the comm tower back on-line."

"General?" Shepard presumed, walking up the ramp into the prefab.

"Commander Shepard." He recognized, though he didn't look up from his console. "Got reports that you were coming, but I couldn't believe it. General Corinthus." He introduced himself.

"I've come to get Primarch Fedorian." She told the General.

That simple statement pulled Corinthus's attention away from his command terminal. "Primarch Fedorian is dead. His shuttle was shot down two hours ago as he tried to leave the moon."

"Damn." Shepard cursed. "That's going to complicate things. What do we do?"

"The Turian Hierarchy has very clear lines of succession." Liara spoke up.

"Right." Shepard nodded. "General?"

"Your friend is right, our lines of succession are very clear." Corinthus began. "However, our comm tower is down, so getting a message back to Palaven Command to request the information is not possible, not until the tower is operational again. To make matters worse, Husks are swarming that area. We can't get close enough to repair it."

"Don't worry, General, we'll get that tower operational." Shepard stated, grabbing her assault rifle.

"Thank you, Commander." Corinthus nodded.

"Alright, let's move out!" Shepard ordered her squad.

The team proceeded out of the base camp, and towards the large satellite dish sticking out of the ground. Closing in on the tower, the team immediately opened fire, ripping apart the Husks that swarmed at the tower's base. Once the Husks were taken care of, Shepard walked over to the tower's control panel, and typed in a few commands. A warning symbol flashed, and Shepard shook her head.

"We can't repair it from here." Shepard turned around to face the team. "Doctor, you're up."

The Time Lord nodded. "Right. Keep the Husks off me, and I'll work my magic." He climbed onto the ladder, and to the top of the tower. He removed the panel sheltering the electrical components from the elements, and examined the electrics.

It seemed the reason for the tower's inoperable state were several loose wires, knocked out of their sockets by powerful shaking, probably caused by a Reaper's footsteps. The Doctor reconnected the wires to the proper nodes, and to ensure that this didn't happen again, he fused the wires into place using the Sonic Screwdriver to essentially solder the wires.

"Okay, I'm coming back down!" He informed his comrades, who were firing upon incoming Husks. He proceeded back down the ladder, and joined his allies in taking care of the Husks.

"General, do you read me?" Shepard radioed. "The comm tower's back on-line."

 _"Much appreciated, Commander. I'll contact Command."_

"Understood, we're on our way back." Shepard responded, closing the channel. She began leading the team back to the base camp, along the way aiding a wounded Turian squad they came across. The camp's barricade lowered, allowing them entrance, and Shepard walked back to Corinthus's position.

"Commander," Corinthus greeted as Shepard walked up the ramp, "I've just received word from Command. There are so many dead or MIA, Command's still having trouble determining who it is."

"Well, I don't care who, as long as they can get me the help I need." Shepard responded.

"Don't worry, Shepard, we'll find you the Primarch." A Turian assured, walking up the ramp into the prefab.

"Garrus!" Shepard smiled.

"Vakarian, sir-I didn't see you arrive." Corinthus saluted.

"At ease, General." Garrus responded, causing Corinthus to relax.

"Garrus, am I glad to see you." Shepard walked up to him. "We thought you were still on Palaven."

"If we lose this moon, we lose Palaven." Garrus outlined. "I'm the closest damn thing we have to a Reaper expert, so I'm... advising." He said the word with distaste, obviously wanting to be fighting the Reapers instead of being in an advisory position.

"Good to see you again, Garrus." Liara smiled.

"You too, Liara." Garrus returned. He then turned back to Shepard. "General Corinthus filled me in. We know who we're after."

"Palaven Command says the next Primarch is General Adrien Victus." Corinthus relayed.

"Victus? His name's crossed my desk." Liara recognized.

Shepard turned to Garrus. "Know him?"

Garrus nodded. "I was fighting alongside him this morning. Lifelong military." Garrus outlined. "Gets results, popular with his troops. Not so popular with military command-he has a reputation of playing loose with expected strategy."

"What do you mean?"

"On Taetrus during the uprisings, his squad discovered a Salarian spy ring about the same time the Sepratists did." Liara explained for Garrus. "Rather than neutralize the ring, he fell back. He even gave up valuable fortifications, which the rebels took."

"Then the rebels attacked the Salarians." Garrus continued. "And when both groups had been worn down, Victus moved in. Didn't lose a single man."

"Bold strategy," Corinthus conceded, "but wild strategy doesn't get you advanced up the meritocracy."

"Primarch Victus." Garrus chuckled. "That'll be something."

"Think he can get the job done?" Shepard inquired.

"We both know conventional strategy won't be enough to defeat the Reapers. Right now, he could be our best shot. And I trust him." Garrus nodded once more.

"Okay. Let's get him on the shuttle, and get him out of here." Shepard outlined.

 _"Commander!"_ Shepard's comm crackled, and Joker's voice filled her ears. _"Shepard, come in!"_

"What's the situation, Joker?" She responded, pressing her fingers to her ear.

 _"We've got a situation on the Normandy, Commander."_ The helmsman explained. _"It's like she's possessed; shutting down systems, powering up weapons. We can't find the source."_

"Liara," Shepard turned to the Asari, "Go back and take a look." She ordered. Liara nodded, and ran back to the shuttle. "Garrus, you said you were with Victus this morning?"

"Yeah, but we got separated." Garrus outlined. "He went back to bolster a flank that was breaking. He could be anywhere out there."

"We're trying to raise him now, Commander." Corinthus informed.

"Incoming Harvester!" Vega suddenly yelled, pointing in the direction of the Harvester. The Harvester flew over the camp, disregarding the troops inside, and flew in the direction of the airfield. "It's heading for the airfield!"

"General, keep trying to raise Victus. Tell him we'll rendezvous here." She ordered. "In the meantime, my team an I will take care of that thing. Coming Garrus?"

"Are you kidding?" The Turian responded, unfolding his sniper rifle. "I'm right behind you."

With everybody ready, the team proceeded towards the airfield.

* * *

By the time the team reached the airfield, the Harvester was long gone, leaving only a small group of Husks and Marauders behind, which were easily taken care of. Upon dealing with the Husked forces, the team was contacted by Corinthus, who informed them that the main barricade was dangerously close to being breached. With that in mind, the team hoofed it back to the base camp, and Shepard took control of the large turret gun on top of the barricade. She immediately began opening fire on the Reaper forces, killing them before they even made it to the barricade.

Until a massive Husked... thing jumped down from a cliff, landing in front of the barricade, and causing a massive quake.

"Holy hell!" Vega yelled, pumping the massive brute full of lead. "What the hell is that thing!?"

The Brute then charged forward, heading straight for the barricade. It hit, causing the barricade to shake, and Shepard to fall off.

"Oh shit!" Shepard yelled, opening fire on the Brute.

Powerful incineration blasts, grenades, and a whole lot of bullets lanced through the air, all heading for the Brute. But the massive beast kept soaking them up like a sponge, undeterred.

Then, Shepard noticed something. "The neck!" She yelled. "Aim for the neck!"

The Brute's neck was very thin, just big enough to support the Turian head the Brute had. But it also appeared to be very weak.

The combined shots from the team tested that theory, as the bullets ripped through the Brute's metal neck, severing the head from the body, and the body toppled over, lifeless.

"Damn." Vega breathed. "I've never seen anything soak up that many bullets."

"Just wait until you see a Dalek." The Doctor told the man.

 _"Shepard, Corinthus here."_ The Turian General radioed.

"Any word on the Primarch?" The Commander inquired.

 _"Still can't get a stable comm-link."_

"Okay. I'm going on foot. Shepard out." She finished, closing the link. "Garrus, take us to the last place you saw Victus."

Garrus obligingly nodded, and took point. He led the team into the trenches along the edges of a series of steep cliffs, roughly west of the base camp.

"How far?" Shepard asked, running behind Garrus.

"Should be pretty quick." He answered. "Unless we find trouble."

They all pushed forward, passing by a few deceased troops, taken out by the Reaper forces.

"Damn it." Garrus suddenly cursed. "Look at Palaven." He prompted, causing the squad to look up. Palaven's surface was even worse than it had looked on the shuttle. The massive blazes of fire and explosions were bright enough to illuminate the side of Palaven not facing its sun. "That blaze of orange-the biggest one-that's where I was born."

"...I'm so sorry." Having seen his home burn before in a seemingly hopeless war before, the Doctor could definitely sympathize. Still, the Reapers couldn't even come close to the horrors the Doctor had seen in the Time War. "Do you still have family there?"

"My dad, and a sister." Garrus nodded sadly.

"How bad is it?" Shepard inquired.

"Three million dead the first day, five the second." He recited.

"What about your military?" She continued.

"Look around." Garrus despondently responded. "That should give you some idea."

"Still, you're putting up a good fight." Shepard pointed out, as she and the others climbed up a small ledge.

"For now. But how long's it take until the fight gets beaten out of you?" Garrus sighed, and shook his head. "If only they listened to your warnings about the Reapers. We could've been better prepared."

"Maybe." Vega interjected. "But how do you prepare for something like this?"

A duo of Husks suddenly screeched, and came over the cliff's edges. The team reacted instantly, firing upon them, and the two husks behind the first duo. The Husks dropped dead, and fell off the edge of the cliff.

"Shit, I hate those things!" Vega shivered. "And New York is crawling with the creepy bastards!? Never should've left Earth."

"It's gonna be bad all over." Garrus responded, as they all jumped across a gap.

"Leaving the fight just pisses me off." Vega growled.

"But you're here to ask Victus to do the same thing." Garrus pointed out. "Leave the fight to make nice in some boardroom."

"This summit is the only chance we've got." Shepard stated. "None of us are beating the Reapers alone."

"Again, Time Lords." The Doctor coughed.

The team climbed up another ledge as a Harvester flew overhead. There was a squad of Turian soldiers, nearby a downed fighter.

"Soldier, you okay?" Shepard addressed.

"Yes sir, we'll be okay." The Turian responded.

"Have any of you seen General Victus?" Garrus inquired.

"Half hour ago." The Turian soldier answered. "He was headed south."

"Okay." Garrus nodded. "Good luck."

"Yes sir." The other Turian saluted.

"Come on, Shepard." Garrus directed. "He should be this way." Garrus took point.

As they were walking along, a Harvester shot down a Turian fighter, making it crash directly in front of them.

"That was a little closer than I'd like!" Garrus said, once the explosion cleared.

"I'll say." Vega breathed.

Shepard crashed, and shook her head. "No survivors."

"Crash like that, it's not surprising." Garrus stated, leading them down a series of small ledges. "Come on, we shouldn't be too far."

"So, Shepard," Vega suddenly piped up, "Do you think this summit will actually work? Asari? Salarians? Where's the Krogan and Batarians? Where's the meat?"

"It's not that easy." Shepard shook her head.

"Contrary to what you might think, the Batarians actually took the brunt of the initial Reaper attack, so there's not much left of them..." Garrus explained for her. "And the Krogan haven't forgiven any of us for the Genophage."

"Right. The Turians sterilized them." Vega remembered.

"The Salarians engineered it." Garrus reminded him.

"And the Krogan hate them both for it." Shepard continued.

"So they won't be joining us." Garrus finished.

"Too bad." Vega lamented. "I fought with a Krogan. Tough sons of bitches."

The team finally came up on the camp, and two Reaper drop pods fell out of the sky, landing in the camp.

"That sounds bad!" Vega yelled.

"Double time!" Shepard ordered, racing forward. "No Reapers are taking this Primarch from me!"

The team rushed into the camp, past the barricade, into the open area where the drop pods had landed. The team pushed into the camp, steamrolling the Reaper forces that tried to assault them.

All of the forces, except for the Brute. The Brute was angry, flipping over the prefabs, and crushing the Turian soldiers unlucky enough to be close to it when it charged.

"Shepard!" River yelled grabbing the Commander's attention. "I found this! Use it!"

Shepard turned around, and had a gun thrown at her. She reacted fast enough to catch it, and turned back to face down the Brute. It was charging now, so Shepard took the strange weapon, aimed it at the Brute, and pulled the trigger.

The gun took a moment to charge, but once it did so, a dark purple, almost black, sphere shot out of the gun, and hit the Brute. The sphere then exploded in a massive light display, and the Brute was vaporized.

Shepard looked down at the gun with surprise. It looked like a miniature Reaper leg, mounted on top of a stock. Her hud highlighted the weapon, and identified it as the Reaper Blackstar.

"So that's why they call them that." Shepard muttered. She shook herself out of her amazed stupor, and handed the gun back to River, remembering that it was one of the guns on her list. Then, Shepard approached the command center.

The ramp lowered, allowing a Turian in red and black armor to walk down, and approach Shepard.

"General Victus?" Shepard asked.

"Yes." Victus responded, stopping in front of the team.

"I'm Commander Shepard, of the Normandy." She introduced.

"Ah, Commander," He recognized, holstering his assault rifle, "I know who you are. I can't wait to find out why you're here." He turned to Garrus. "Vakarian, where were you?"

"Heavy Reaper unit on the right flank." Garrus responded. "I believe your exact words were 'Get that thing the hell off my men.'"

"Appreciate it." Victus responded.

Shepard cut straight to the chase. "General, you're needed off planet. I've come to get you."

"It will take something beyond important for me to leave my men, or my Turian brothers and sisters, in their fight." Victus stated.

"Fedorian was killed." Garrus told him. "You're the new Primarch."

"There's a war summit being held. I need you there to represent your people so we can find some way to end this war." Shepard explained.

Victus didn't say anything. He pushed past the team, and came to a stop, looking up at the looming, burning visage of Palaven. "I'm Primarch of Palaven?" He breathed, nary believing it. "Negotiating for the Turian Hierarchy?" Victus looked away from Palaven, and towards Shepard. "I spent my whole life in the military, I'm no diplomat... I hate diplomats."

"I don't need you to be a diplomat." Shepard shook her head. "Right now, what the galaxy really needs are people who've had first hand experience with this war. Who've been through this hell."

"I like that. You're right." Victus sighed. "Give me a moment to say goodbye to my men." He requested. Shepard nodded, and Victus walked off to do just that.

Garrus walked over to Shepard. "Without him down here, there's a good chance we lose this moon."

"Without him up there, there's a good chance we lose everything." Shepard retorted.

Garrus turned his head, looking at one of the Reapers walking around. "Look at that! And they want my opinion on how to stop it? Failed C-Sec officer, vigilante... and _I'm_ their expert advisor?" Garrus sighed. "Think you can stop this, Shepard?"

"I don't know, Garrus." She honestly replied. "But I'm sure as hell going to give it my best shot."

"I'm damn sure nobody else can do it. For what it's worth, I'm with you." Garrus stated.

Shepard smiled. "Welcome aboard." She shook his hand. She then turned to Victus. "Are you ready, _Primarch_ Victus?"

Victus turned around, and approached the group. "One thing." He began. "Commander, I understand your need for our fleets, but I can't spare them. Not while Palaven's burning. But if the pressure could be taken off Palaven..."

"That's a pretty tall order." Shepard crossed her arms.

"We need the Krogan." Victus was blunt. "I can't see us winning this without them. Get them to help us, and then we can help you."

"The Krogan..." Shepard repeated.

Garrus mandibles flared out in the Turian version of a smile. "Looks like your war summit just got a lot more interesting..."


	35. From Ashes

With the mission on Palaven over, the team returned to the Normandy, and went back to their assigned posts, while Shepard dealt with the war summit. The Doctor, however, stalked off to Starboard Observation, and set back to work on decoding the plans for the Moment. The fact that he was again working with a weapon known as such to defeat a seemingly invincible enemy bothered him somewhat, but he couldn't dwell on it. Actually, the simple fact that he was working to destroy the Reapers bothered him as well. Hundreds of thousands of civilizations were harvested. Their knowledge, their cultures, everything that made them unique was still there, just... locked away. Shouldn't they be finding a way to talk to the Reapers, get them to step down peacefully, and share their knowledge with the rest of the galaxy?

No, the Reapers were abominations. They twisted and consumed whatever they touched. And the species that comprised the Reapers had long since been dead. While he continued on working, the intercom suddenly bleeped.

"Doctor," Samantha Traynor's voice filtered out, "I have an urgent communication for you from Admiral Hackett."

The Time Lord's eyebrows raised. "Me?"

"That's correct. Forwarding it to the comm room."

The Time lord's curiosity had been piqued. He had heard about the good Admiral from Shepard, enough to know he didn't call unless it was important. So, he got up from what he was doing, and headed up to deck two.

Once the Doctor passed through the threshold into the comm room, he was met with the life-size projection of the distinguished man.

"Doctor." Hackett greeted, snapping off a respectful salute, even though the Doctor wasn't technically military. "A pleasure to finally meet you."

"And you. Forgive me if I don't salute, not my style, you understand."

The corner of Hackett's lips twitched. "I know. I've read yout files."

The Doctor faked being shoked. "Oh, I have files. Which one was your favorite, the living plastic?"

"The Yetis in the sewers, actually." The Admiral corrected. He then shook his head. "As much as I'd like to talk about old files, we should get down to business."

"Right." The Doctor nodded. "I assumed this wasn't a social call."

"Unfortunately, that"w's exactly right." Hackett sighed, and his expression went grim. "Tell me, what do you know about the Cybermen?"

"That they're ruthless conquerors hell bent on converting all life into more of themselves, or failing that, destroying it. But from what I understand, you lot took care of them and then erased all evidence that they ever existed."

Hackett rubbed his forehead, as if trying to alleviate a headache. He sighed, and continued speaking. "The Cyber Wars were one of the most turbulent parts of human history. After the Cybermen were finally vanquished, and humanity entered the galactic scene, the records were altered. Devastating Cyberman attacks became terrorist plots, and it was all quietly buried."

The Doctor frowned. "Why would you hide something like that?"

Hackett launched into another explanation. "After learning about the quarians, of how they created the geth and were kicked off the Citadel for it, we didn't want the same thing happening to humanity, not so soon after we joined galactic polotics. Even though the Cybermen weren't technically AI, and we had no knowledge of those laws, wars had been started over less, and we couldn't risk it."

"I understand the reasoning, but that doesn't explain why I'm talking to you."

Hackett looked around, as if checking to make sure he was alone. "One of our colonial garrisons reported an attack by Reaper forces of unknown type. Their description matched the Cybermen almost exactly."

The Doctor's brow shot up as his eyes widened. "They're working for the Reapers?"

Hackett shook his head. "We don't know. Reaper ground units are rarely seen without an actual Reaper nearby. It's possible they're working with the Reapers, but I think the Cybermen are using the Reaper invasion as a smokescreen."

"Hiding their operations by making it look like the Reapers are responsible." He nodded.

"Exactly. But no matter which way we look at it, it's bad news. If they are back in force, then I don't need to tell you that a two front war would be the last thing we need right now. Along with Reaper-enhanced Cybermen."

"So, why are you telling me this?"

"I need someone to investigate, and with Shepard busy trying to rally the galaxy's forces, you're our best shot."

"I don't take orders from you."

Hackett crossed his arms behind his back. "Doctor, do you really expect me to believe you'd abandon humanity in our hour of need?"

"...no. But if I'm going to do this for you, I'll need to borrow a few people from the Normandy's crew."

Hackett simply nodded in response. "I can authorize a temporary transfer to your command as you see fit."

"Good, thank you. Now, what's this colony I'm supposed to go to?"

"Eden Prime."

"Eden Prime, isn't that where this whole business began?"

"Indeed it is. Do you need transport?"

The Doctor shook his head. "No. The TARDIS isn't back up to a hundred percent, but short hops within the galaxy should be fine."

Hackett nodded."I'll leave you to it. Hackett out."

The Doctor shook his head, briefly contemplating the mess he was about to get into, as he headed down to the lower decks in search of Susan and River.

Later, on board the TARDIS...

Susan strode into the console room, stretching her arms. "I'm glad to finally be out of that uniform, it was itchy. So, what's this colony we're heading to again?"

"Eden Prime." River answered, in a hardsuit and checking over her weapons. "It's where Shepard discovered the prothean beacon that gave her the vision of the Reapers."

"I see... so, in a way, we've come full circle?" Susan concluded.

"I suppose, in a way." The Doctor agreed as the TARDIS's engines ground to a halt and the ship materialized. "Now then, let's go see what's out there..." He said, taking charge out the doors.

The door shut behind Susan, who was last out, and the three looked over the colony. It was, quite simply, beautiful, like a scene out of a painting.

Waterfalls out of the sides of distant cliffs cascaded, feeding one massive river in the distance. Rolling hills, covered in thick canopies of trees stretched into the horizon, and large metal towers jutted out of the ground, touching the sky. Something was amiss, however.

"Where is everybody?" Susan questioned, quite rightly.

Though the TARDIS had landed in a settled area, given away by the prefabs set up quite close to each other, the people that were supposed to be inhabiting them were gone.

But the Doctor knew exactly what had happened to them. "This was the site of the Cyberman attack Hackett told me about. Everyone that was here is either converted by now, or..."

"Dead." River finished.

"But why attack this place?" He frowned. "If they were trying to convert as many as possible, they would have attacked a larger settlement, unless..."

"They were here for something else." Susan concluded.

"Right." The Doctor nodded. "Why don't we walk around, and take a look?"

Before they could start moving however, Susan froze up.

"Susan?" The Doctor approached her with worry. "What's wrong?"

"Do you hear that?" Susan whispered.

"Hear what?" River frowned.

"Shh!" Susan shushed. " _Listen_."

The Doctor closed his eyes, and tried to listen out for what Susan was hearing. After a short while, he could hear it.

Loud hydraulic clanging, as if being made by an army of marching metal men, was getting closer and closer to the three.

"The Cybermen... They're coming!" He breathed in fear. He grabbed hold of Susan and River's wrists, and pulled them along. "Come on! We need to find what they were looking for before they get here!"

As they ran along the dirt paths, Susan pointed something out. "Look. The colonists was excavating here."

Indeed, a large quarry was slap-bang in the middle of the outpost. Towers, seemingly made of Prothean technology, stuck out of the ground.

"You think they found something in there?" River suggested.

"Maybe." The Doctor agreed. "It would explain why the Cybermen chose to waste their time on such a small outpost."

The three continued through the area, and came to a metal outcropping, with a control panel facing them.

"It's an elevator control." River pointed out, walking over to it. "Whatever the colonists found is still on board. Let me bring it up." She tapped a few commands into the panel, and the floor beneath them shook slightly as the elevator engaged. The elevator came up to their level, and halted.

The three's eyes widened as they saw what was on the platform.

"It's prothean." River breathed.

"No... it's _a_ prothean." The Doctor corrected, slowly walking onto the platform.

"But that can't be right. They died out fifty-thousand years ago!" Susan stated. "Even for Time Lords, it's impossible to live that long."

"That's because it's not alive. But it's not dead either." The Doctor explained, scanning it with the sonic. "Not fully. Stasis capsule, that's what this thing is. Keeping it's occupant comfortably asleep for the past fifty millennia. It must smell terrible in there."

"Didn't the Reapers turn the protheans into the Collectors?" River asked. "Is that what's in there?"

The Doctor shook his head. "No. This is an original, unmodified prothean, fully intact. Liara's going to have a fit."

"That doesn't seem possible." Susan said, looking at the pod.

"Shepard saw prothean stasis capsules on Ilos." The Doctor said, stepping even closer to the pod. "Those failed due to insufficient power, but this one's power has been continnuously running for all that time, keeping the prothean popsicle inside stable. If they chose this one to put into stasis... they must have been greatly revered."

"So, can we open it?" River asked.

The Doctor pursed his lips, and peered at the pod's single control panel on the front. "I think so. We'd have to, in fact. The pod's entirely dependent on the facility below for power, the moment we disconnect it..."

"The power fails." River continued.

"And the prothean inside dies." The Doctor concluded.

"So, let's crack this thing open." River said stepping forward.

"No!" The Doctor blocked her. "Physically breaking it open would kill him. We need to send it the command signal, the password. if you'd like."

"The labs nearby could have what we're looking for." Susan stated.

The Doctor nodded at the suggestion, and the three stepped off the elevator. Suddenly, an explosion tore through one of the prefabs in front of them, kicking up dirt and heat.

When the dust had settled, a legion of Cybermen stood on the other side.

One stepped forward of the group, and began speaking.

"Non-human presence detected!" The Cyberman proclaimed. "You are incompatible! You will be deleted!"


	36. March of the Cybermen

"You will be deleted!" The Cybermen echoed, as they raised their arms, with the intent to fire.

River was quick to act fast. She unholstered a singularity grenade from her belt, and threw it into the crowd of Cybermen. It went off, and created a singularity, picking up some Cybermen in the process. The singularity ate away at their thick metal armor, exposing some of their weaker innards.

River then took the pistol at her side, and fired at the torsos of each one, aiming for the Cybermen's power sources. Only a few shots hit right on target, but it was enough to cause a chain reaction of explosions, taking care of the Cybermen in the singularity.

It only seemed to agitate the other Cybermen, however, if a Cybermen could experience such a thing.

"Delete! Delete! Delete!" The other Cybermen cried as they marched forward.

The three organics dove behind cover.

"Great job, River, you just managed to anger the Legion of Cybermen!" The Doctor yelled, as a laser blast came close to his head.

"Don't worry, I have a plan!" She responded, taking another grenade from her belt, and throwing it into the group.

It detonated, freezing four of them in place. The cryo grenade had managed to turn the metal armor of the four Cybermen brittle enough to be shattered by the four gunshots that followed, causing the frozen Cybermen to topple to the ground, headless.

River took the assault rifle she had holstered, and activated its incendiary ammunition, aiming for the heads of the remaining Cybermen, and the parts of their bodies not covered in the thick metal armor plating, while the Doctor and Susan ran interference using their sonic screwdrivers.

By the end of the short battle, all of the Cybermen lay on the ground, dead.

"I think that's all of them." The Doctor said. "For now. Come on, let's find that lab."

The three headed towards the edge of the compound, passing through the buildings, until they came to one with a locked door that had to be the lab.

The Doctor bypassed the door using the sonic screwdriver, and headed inside.

Approaching the computer terminal on the wall, the Doctor tapped in a few commands, seeing what the terminal had stored. It began playing back a recording of organic ground troopers fighting the reapers, but these were... different. They were bipedal, that much was obvious, they were wearing odd suits of armor unlike anything else in the galaxy, and their heads... they looked almost like Collectors.

' _The Protheans._ ' The Doctor thought to himself.

As he watched the video, he was suddenly pulled into a memory.

 _The bunker was breached. The enemy had found them. Thousands were already dead, many more were missing. Unless the remainder entered stasis now, the Protheans' total extinction was certain._

 _He and his troops valiantly fought against the... abominations the others had become._

 _But even then, he and his men were being pushed back. A shot from one of the indoctrinated tore into Kaang, killing him. Enraged, he called upon his biotics to push them back, killing them with the sheer amount of raw power he commanded._

 _He ran over to Kaang, picking up his fallen comrade's form. "Victory, seal the bulkheads!" He commanded, dragging the body behind the closing blast doors._

 _The door sealed with a clang, and he let go of Kaang's body. He turned around, and looked at the columns of fire climbing up the sides of the bunker._

 _"How many?" He demanded of Victory._

 _"Approximately 300,000 lifepods have been destroyed." The VI reported._

 _He approached a lifepod, tapped in the command code, and watched as it opened, revealing the charred corpse of the commander._

 _"A third of our people..." He sighed, placing his hand on the shoulder of the corpse, he sent a silent prayer to the gods._

 _"Alert!" Victory suddenly flashed, startling him out of the prayer. "North side bulkhead could not be sealed, hostiles inbound!"_

 _"Then all forces to the north!" He commanded, taking charge, and leading the remaining troops forth._

Suddenly, he took in a sharp inhale of air, and the Doctor was back in reality.

"What..." He began, heavily breathing. "Was that?"

"What do you mean, grandfather?" Susan questioned. "It was just static."

"It was like... I was having a flashback." The Doctor frowned. "But it wasn't _me_ in the flashback. I was a Prothean."

"Of course..." Susan seemed to realize something. "Grandfather, when Compassion helped sort out Shepard's memories, didn't you act as a bridge? To prevent Shepard's brain from being overloaded?"

"I did... You don't think I accidentally got Shepard's cipher?" The Doctor wondered.

"Explains how you could understand all of that." River concluded. "Did you see the pod's command code?"

"Part of it, but not all of it." The Doctor said. "Let's see if we can go find the rest of it."

The three headed towards the other end of the colony, to the other lab. While they were cutting through the center, a voice suddenly echoed through the colony.

 _"All cyber-units,_ " The synthesized voice of a cyberman announced, _"converge on Prothean dig site alpha."_

"That doesn't sound good." Susan stated.

"I don't think we'll be able to take on a full cyberman army." River said. "Let's go find the command signal before they get here."

The team picked up the pace, and headed into the next lab. The Doctor found the terminal, and entered the activation command. A video started up, and he was pulled into another memory.

 _They were walking through the bunker, heading towards what empty lifepods were left. The immediate threat had been dealt with for now, but the enemy was patient. The only hope for survival now, was to outwait the enemy._

 _"I never believed our empire would fall." Jaal said next to him._

 _He stopped, turning to face the other Prothean. "So long as one of us remains, it has not fallen. We will sleep, until the Reapers return to dark space. Then, we shall return, a million strong!"_

 _Jaal nodded. "For the empire."_

 _"For the empire." He responded. "Get to your stasis pod."_

 _Jaal nodded, an ran off to his pod._

 _"Victory, send out the readiness signal to the other lifepods." He commanded._

 _Victory flickered into existence beside him. "And the refugees that have yet to reach the bunker?"_ _He stayed silent for a few moments. "They will be remembered."_ _Suddenly, the bunker shook, as more of the indoctrinated appeared._

The Doctor shook off his disorientation as the weight of the new memories filling his mind. "I think I have the signal the Protheans used now. Let's head back to the pod."

Susan and River nodded, and followed the Doctor's lead.

They approached the pod, and the Doctor accessed the control panel. He typed the code in, sent the command signal, and stepped back.

The pod hissed, and let out spurts of cold, fifty-thousand year old air as it opened, revealing the Prothean inside.

"Hmm..." River peered into the pod. "It may take some time for him to-"

The Prothean's eyes suddenly shot open, and he looked around. He looked at Susan first, then River, before finally focusing on the Doctor.

His biotics flared up, and he pushed the three away. He slowly, but desperately, tried to climb out of his pod. His leg caught the edge, and he fell. As he looked up, he finally noticed the state of the planet around him, and froze. His mout parted in shock, and he slowly came to his feet.

"Careful," The Doctor told the others as they walked back over, "he's disoriented. He may not know where he is." He approached the Prothean. "Hello," The Time Lord greeted, "I don't want to hurt you, I'm the Doctor." He held out his hand, and the Prothean looked at it for a moment, before reaching out and making contact. Suddenly, the Doctor was in another memory.

 _"...a few minutes!" He demanded, turning to face victory._

 _"No." The VI shook its head. "There is no other option."_ _"_

 _There are other pods online!" He retorted. "Those soldiers are still alive!"_

 _"Their sacrifice will be honored in the coming empire." Victory stated. "Preparing neutron bombardment. Get to your pod."_

 _He clenched his fist, but relented. He ran over to the pod, and it opened, allowing him to lay down inside._

 _"Neutron bombardment underway." Victory reported, as the massive explosions shook the pod._

 _"The bunker is secure, Commander Javik." Victory reported as the explosions stopped._

 _"What is left of it." He corrected. "A few hundred people. How am I to rebuild the empire from that?"_

 _"Further adjustments may be necessary." Victory stated. "The neutron purge compromised the facility."_

 _"Clarify." He demanded._

 _"Sensors offline." Victory began. "Automated reactivation is no longer an option. You will remain in stasis until a new culture discovers this bunker. This may lead to a power shortage."_

 _"Do not shut off more pods!" He demanded. "I need the few that are left!"_

 _"Power needs will be triaged appropriately." Victory stated. "You will be the voice of our people._ _"_

 _"I will be more than that." He retorted as he slipped into unconsciousness._

The connection broke and the Doctor staggered back as the Prothean, apparently named Javik, fell to his knees.

"How many others?" Javik questioned, not wasting a single moment.

"Just you." The Doctor told him. "When I touched you, I saw..."

"Our last moments." Javik stated, standing back up. "Our failure."

"I'm sorry." The Doctor told Javik. "I know what it's like. To be the last of your kind."

"Hmm." Javik snorted, saying nothing. After a moment, he spoke. "I suppose I owe you my gratitude, Time Lord."

"You know what I am?"

"Yes." Javik nodded. "Your people were formidable."

"Doctor!" River spoke up. "There's a massive group of Cybermen heading our way."

Javik frowned. "The Cybermen? They are here?"

"You know of them?" Susan asked.

"There were legends about them, in my time." Javik explained. "The empire fought a great war with them before the Reapers arrived."

The Doctor frowned. "That can't be right. The Cybermen didn't exist back then, unless..."

"Unless what, grandfather?" Susan questioned.

"I can explain later." The Doctor brushed off. "We should get back to the TARDIS. Javik, if there is anything in that pod you need, I suggest you grab it now."

Javik nodded, and walked back over to the pod. He took his particle rifle, and an oddly shaped... thing out of a storage compartment.

The Doctor nodded, and the four broke out into a sprint, back toward the TARDIS's landing site.

The Cyberman marched into the outpost in force, narrowly missing the four as they entered the TARDIS and took off.

Once Cyber-unit approached another, and began speaking. "The Prothean has escaped."

"Unacceptable." The other stated. "The Prothean must be located at all costs. It is the only being in the galaxy that knows the location of Mondas."

"We will increase our efforts. Mondas must be found."

"We will reach the promised land!"


	37. Interlude: The Normandy II

_"Doctor."_ Admiral Hackett greeted, flickering into existence in the Normandy's comm room. _"I've just recieved the report you sent me. Are you serious? You found an actual, living Prothean, Javik?"_

The Doctor nodded. "Indeed we did. His presence was the reason why the Cybermen chose to invade Eden Prime in the first place."

 _"I see."_ Hackett then frowned, and rubbed his chin in a contemplating gesture. _"Although, it does make me wonder what interest the Cybermen have in Javik. Conversion, maybe?"_

"Maybe." The Doctor shrugged. "Although, invading a planet seems like a lot of effort to go through just to convert a single person. There is something that may give us a hint to their motives." The Doctor brought up his omni-tool, entered a few commands, and watched as a planet was projected next to him.

 _"Is that Earth?"_ Hackett questioned. Indeed, the planet looked identical, only upside-down.

"Close." The Doctor stated. "This is Mondas. Earth's twin planet, and the homeworld of the Cybermen. Well, one of them."

Hackett frowned. _"I don't follow."_

The Doctor took in a breath, and began explaining. "Think of it as parallel evolution. The Cybermen are the product of countless different races, all with the technology and the lack of restraint to eventually turn into the Cybermen. I've seen it before. Telos, Marinus, Planet 14, Mondas, your version of Earth, all of them inhabited by vastly different organisms that all gave rise to the Cybermen... All roads lead to Rome if you'd like."

 _"I understand, but what's the significance of that now?"_

"Admiral, I believe that the Cybermen we fought on Eden Prime weren't the Cybermen created by Cybus Industries, but Mondasian."

 _"But they were indentical to the Cybermen Cybus created. How can you be sure?"_

"Ah, that's where you're wrong." The Time Lord began. "You said you recieved the initial descriptions from the colonial garrison of Eden Prime. They missed a vital detail. The Cybus Industries logo was entirely missing. If they were the Cybermen created by Mr Lumic, that logo's written into the schematics, every Cyberman ever created would have it. Instead, the part of the chest where the logo ought to be was blank."

 _"So they're not the Cybermen humanity created. That's a tremendous relief. The last thing we needed were the other races refusing to work with us because they were attacking."_ Hackett stated. _"In any event, I'm pleased to report that the Cybermen have completely withdrawn from Eden Prime. And they left most of the population intact as well."_

The Doctor just shook his head. "You may think that's a victory, but you know as well as I do that they won't rest until they have what they want."

 _"I do, and that's why, until further notice, I'm authorizing Javik to be posted on the Normandy. With its stealth systems, and how often it moves around, the Normandy is the safest place for him to be right now."_

"You think he'll agree to that?"

Hackett nodded. _"He's a soldier, and the last of his kind. Right now, the only familiar experience for him is likely fighting the Reapers. The Normandy can, hopefully, give him a chance to integrate."_

"I'll tell Shepard, then."

 _"I'll leave you to it. Hackett out."_ With that, the Admiral flickered out of existence, and the Doctor headed down to deck four, where Javik was waiting.

The Doctor strode into the port side cargo hold, where apparently, Javik had drawn a crowd.

Two marines stood, blocking Liara from approaching the Prothean, and Shepard stood further back, simply watching. As the Doctor walked in, she turned to face him.

"So, a living Prothean." Shepard began. "And I thought _I_ found the wierd ones."

"I tend to have a habit of bringing home strays," The Doctor shrugged, "the missus hates it. What's the issue?" He asked, watching Liara angrily argue with the two marines.

"Liara wants to bombard him with questions, but first contact protocol says 'don't attack, but assume hostile intent.' Guess we have Shanxi to thank for that." Shepard shrugged. "Is he safe?"

The Doctor looked over to Javik, who was kneeling on the floor in some sort of meditative state. "He's fine. If he was actively hostile, he could've turned everyone in the room into a fine red mist by now."

Shepard nodded, and she turned to face the marines. She gestured without speaking, and the two marines saluted, before clearing the room.

Shepard stepped forward. "I'm Commander Shepard, captain of this ship. You are?"

Javik did not answer at first, but he opened his eyes, and stood up. He seemed to sniff at the air, and began speaking. "I can smell your fear, your anxiety. The Reapers are winning."

Shepard stepped back. "What do you mean?"

"All life provides clues for those who can read them." Javik said, looking away. "It is a skill that even you may master someday, gallifreyan."

Hearing that last sentence, the Doctor stepped forward. "You said back on Eden Prime that my race was 'formidable.' What did you mean by that?"

Javik blinked. "Your race stood against us when none others chose to do so. We thought you to be easy pickings. The sight of a dozen worlds burning in retribution told us otherwise."

"I see." The Doctor said. "You also said your people had legends of the Cybermen?"

"Yes." Javik nodded. "Though my people knew them by a different name: the metacon. The empire fought a long and bloody war with them, pushing them back to their homeworld. We were victorious, but the war left us drained, when the Reapers arrived, we were easy pickings."

Liara then chose that moment to approach. "We found the archives your people left behind on Mars. They told of how your people surrendered to the Reapers, but not why. I was hoping you could explain?"

Javik looked away from all of them, staring out into space. After a few seconds, he began speaking. "The Silence."

"'Silence will fall when the question is asked.'" The Doctor quoted.

That got Javik's attention, and the Prothean stared, wide-eyed. "You know... How do you know?"

Shepard and Liara looked at the Doctor, almost expectant.

"I've... encountered them before." The Doctor explained. "They're an order, almost fanatics, dedicated to making sure the question is never answered. But that was in my universe... It has to mean something different here."

Javik inhaled. "The Reapers told us it was the end."

"The end?" Shepard frowned. "Of what?"

"Of everything." Javik answered. "All forms of life, all civilizations, not only in the Milky Way, but across the entire universe. All matter in the universe would become dust, the dust would become atoms, and the atoms would become nothing. The Reapers offered us survival, a chance to escape. Some accepted, the rest chose to fight."

"Like you." The Doctor concluded. "So why did you choose to fight?"

"I was born long after the message was sent." Javik explained. "We knew what had happened to those that accepted the Reapers' offer. We refused to let the same fate befall us."

"Hold on," Shepard butted in, "Vigil, the VI on Ilos, said that no offer of surrender was given."

Javik stayed silent. "VI's are not infallible." He waited for a few moments. "Commander, if you would have it, I wish to stay on board this vessel, and continue to fight the Reapers."

Shepard, however, frowned. "You just came from watching your species go extinct, and you want to keep fighting so soon?"

Javik turned away from them, facing the odd little object he'd brought with him, now floating above a table. Javik ran a finger along the strip of light on the tiny object. "This is the echo shard. It holds the combined knowledge of all Protheans, the voices of a trillion dead screaming for vengeance. The Prothean empire will have retribution, I will fight the Reapers, whether or not I am on board this ship, and the only thing the final Reaper hears as it dies, will be the voice of the last Prothean singing victory."

"Well then," Shepard straightened out her uniform, and held a hand out for Javik to shake, which the Prothean took. "Welcome aboard."

Javik nodded, and released his grip. "I look forward to fighting the Reapers alongside you. Now then, I believe I have taken enough of your time."

Shepard nodded. "If you need anything, don't hesitate to ask."

"I will not. Thank you, Commander."

With that, Shepard nodded, and left the room, with the Doctor following close behind, and Liara staying to ask Javik some more questions.

While the Doctor was walking past the medbay, however, he caught a glimpse of someone inside. Someone he hadn't seen since the Collector base.

He rushed inside, and a smile broke out on his face. "Mordin!"

The Salarian turned around in startled surprise, and he smiled pleasantly. "Doctor! Was wondering when you would appear."

"How have you been? I haven't seen you since that business with the Collectors."

"Returned to Sur'kesh, resumed work with STG." Mordin answered. "Shepard looking to cure genophage, came along to help."

"I'm happy to hear that." The Time Lord nodded. "The genophage was a terrible mistake."

"No." Mordin denied. "Genophage correct course of action at time, but current situation requires..." The salarian inhaled, "course correction."

The Doctor frowned, but quickly hid it by changing the subject. "Well, I'm glad you're back. The Normandy was lacking seriously in salarian scientists-turned-stage actors."

Mordin smiled once more. "Should put on production of _Pirates of Penzance._ Will be good for morale."

"We should. Although, it might be hard to find EDI a part."

"Not necessarily. New body produces plenty of alternatives."

"Wait, wait, wait." The Doctor held up his hand. "EDI has a body now?"

"Yes." Mordin nodded. "Currently on bridge with Joker."

"Alright, this I have to see. It was nice talking to you again, Mordin."

Mordin nodded, and turned back to his work. "Should come back soon, could use help."

"I will." The Doctor responded, and he rushed out of the medbay, heading up to deck two.

The Doctor proceeded down the hall, keeping a brisk pace, and entered the bridge.

Joker had already turned in for the night, it seemed, but was a gynoid sat in the co-pilot's seat. Her skin was gray, and her hair looked to be one solid piece. Noticing the entry, she turned to the Doctor.

"Hello, Doctor." EDI told him, standing up to face him.

"EDI." The Doctor greeted, "Mordin told me you got a body, but I needed to see it for myself." He looked her over, examining the finer details of her construction. "Oh, wow. I've not seen an infiltration unit this well-built since Kamelion."

"Thank you." EDI smiled. She was quick on the uptake when it came to human gestures, it seemed. "I am looking forward to testing it in the field."

"I should certainly hope so." The Doctor responded. "You've been cooped up in the Normandy's systems for too long. Although, it seems to be a bit ill-suited to infiltration now..."

"This unit had an artificial skin-sheath." EDI explained. "It was burned off during the crash that disabled it."

"That's a bit unfortunate..." The Doctor frowned. "Although, we could just grow you another one. The TARDIS's medical bay has the equipment for it."

EDI raised one of her eyebrows. "You could grow me organic skin?"

The Doctor nodded. "Sure. It's not hard. Your body would just have to be shut down for a few hours, like an organic being put under anasthesia."

"It would allow me to integrate with the crew more efficiently..." EDI contemplated.

"Take all the time you need to think about it." The Doctor said. "When you come to a decision, just let me know."

"Thank you, Doctor. I will return to my post." And she sat back down in her seat.

With that, the Doctor had finally decided to turn in for the night as well. He walked back into the TARDIS, seeking out his bedroom, and he layed down. The clutches of sleep took him within minutes, and he fell into dreamland...


	38. School Reunion

_He was in his office in Chronos Station, looking over the latest reports on the battles raging at the moment. More colonies were lost, hundreds more starships were destroyed, and here he was, sat in an office far too large for just one man._

 _The galaxy was burning, and he was powerless to stop it._

 _It was not a feeling he liked, being powerless. He always had some degree of control over a situation, no matter how small, but this current situation with the Reapers made him feel that no matter what he did, he was still just playing into their hands._

 _He wouldn't be strong enough to defeat them._ Humanity _wouldn't be strong enough to defeat them._

 _But... there might be someone who could. He tapped in a few comands into the holographic console, and watched as a hologram -all of the Council's data on Gallifrey- flickered to life._

 _He frowned--it seemed the one piece of data he was looking for, the co-ordinates, were classified. Sealed not by firewalls, but physical seperation from the rest of the files._ _It didn't matter, he had ways of getting past that._

 _He tapped a button on the arm of his chair. "Leng, I have a new mission for you. Come to my office immediately."_

 _While he waited, he began drumming his fingers on the arm of the chair._

The Doctor's eyes slowly opened, and he looked around, the details of the dream fresh in his mind. He picked sleep out of his eyes, and looked up at the cieling.

"What was that?" The Doctor quietly questioned. "Trying to tell me something, eh old girl?"

The gentle, steady humming of the TARDIS in the back of his neck was the only response.

The Doctor frowned. The TARDIS didn't often cause him to experience dreams like that. Almost never, in fact. The last occasion the Time Lord could think of was Sarah Jane's wedding, alerting him to that business with the Trickster.

If this dream was anything like that, then something was about to go down. Problem is, when? Or were the banshee circuits playing up again, and there was no real danger at all?

Ah, well, he'd have plenty of time to dwell on that later. For now, it was time to get back to work.

But as he stepped out of the TARDIS, the Doctor couldn't help but think he was missing something. Specifically, the rythm the Illusive Man was drumming out...

 ***Line Break***

A few minutes after waking up, the Doctor had recieved the summons to join the rest of the ground team in the shuttle bay.

There really was no rest for the wicked, it seemed. Fortunately, Time Lords didn't require nearly as much sleep as humans, so the Doctor was ready and able to answer at a moment's notice.

From what Shepard told him, and the rest of the team, Mordin's work on the genophage cure was taking longer than expected, so in the meantime, the Commander decided to check out a distress signal from Grissom Academy, a school for the gifted.

When the Normandy jumped into the system, it easily became apparent why the academy required assistance.

Cerberus was there.

The Doctor wondered how they could have taken a station of such size. Shepard explained that, due to the war's severity, the students would have been sent home, leaving only a small skeleton crew to maintain the station.

So now, they were on a shuttle, with the Normandy providing a distraction allowing the shuttle to sneak in without being detected.

The shuttle docked, allowing the team to exit, and proceed into the station. The academy's head, Kahlee Sanders sent regular status updates to Shepard, guiding them to the server room she was holed up inside.

The team made quick work of the Cerberus troopers inside, and Kahlee opened the door, greeting the Commander.

She quickly explained the situation. The remaining students, who stayed behind to help the war effort, were pinned down with a teacher in Orion Hall.

Wasting no time, the Commander took point, leading the team out of the server room, and towards Orion Hall.

The Academy was mostly deserted. Even the Cerberus force that had assaulted the station was only the crew of a single cruiser. They had obviously expected an easy fight, but now that Shepard was here, she was going to make them work for it.

As they walked through, they were forced to watch a pair of Cerberus troops drag a student by his ankles, the kid screaming as he was pulled along.

Shepard tried to break the glass, but it had been reinforced, in case that section of the station was depressurized. One of the Cerberus troopers noticed this, and barely glanced at her, entirely unconcerned. The door shut behind them, and they were gone.

"Barbaric." Javik commented from his place in the squad.

"I won't let those bastards take any more." Shepard growled, and the Doctor agreed. "Let's keep moving, we're on a time crunch here."

As they kept moving, aa Cerberus announcer tried feeding propaganda over the loudspeakers. It took everything in Shepard not to pump the speakers full of lead.

As they entered the next room, they came across two more troopers trying to get a student to drop his barrier. Shepard didn't hesitate to fire upon them. When the fighting had stopped, the student dropped the barrier, gave the team thanks, told them to be on the lookout for his sister, and scurried off to security.

The team pushed forward, moving through some classrooms and administration areas, pushing through more Cerberus troops.

They found another student, the other student's sister, and sent her to security as well. Then, the team continued forward. They found the path into Orion Hall, and entered.

There, a battle was unfolding between Cerberus and the students, with a powerful biotic coordinating the students. A woman Shepard would recognize in a heartbeat.

"Jack?" Shepard said.

"Shepard?" Jack questioned. Then, the exchange was rudely interrupted by the arrival of a large ATLAS mech.

Seeing the mech getting ready to open fire on Jack, the team opened fire on the mech, drawing its attention.

"Keep that thing off us!" Jack shouted, pushing one of her students up the stairs.

The team dove into cover, popping out every few seconds to fire.

"Doctor!" Shepard shouted. "Got anything to deal with that thing?"

"Sure do!" He changed the setting on the sonic, and peeked out to point it at the ATLAS. He pressed down on the activator, though nothing happened. "I can't do anything while its shields are still up!"

Shepard nodded. "Garrus, EDI, hit it with an overload!"

"Roger that!" "Affirmative!" Garrus and EDI chorused, peeking out to shoot the blasts of energy at the mech.

The mech's shields sparked and spluttered as they fell, giving the Doctor his chance. He pressed down on the sonic screwdriver activator, and the mech's weapons stopped firing.

"It's weapons are jammed!" The Doctor informed the team.

Shepard and the rest of the squad jumped out, and opened fire. Liara hit the mech with a warp, tearing part of its armor, while James hit the mech with a carnage shot. Shepard's was the last blow, as she jumped up and slammed the ground, unleashing a nova.

The mech finally had too much, and it spluttered and kicked out flames. The mech's power core finally exploded, reducing the ATLAS to nothing more than a heap of scrap.

"Kahlee said she was putting out an SOS!" Jack shouted from up top. "I had no idea the Queen of the Girl Scouts would show up!" She turned around to give orders to her students, then jumped down to meet Shepard. She strode up to Shepard, and clocked her across the face. "Damn it, how many times have I told you not to trust Cerberus!?"

Shepard rubbed her cheek. Jack had a mean right hook. "Trust me, you're not telling me anything I haven't told myself."

"Oh..." Jack stepped closer. "Feel bad? Well shit, I guess that's a _big_ comfort to all the people Cerberus has killed!"

"Jack." The Doctor stepped forward. "I see you're as... charming as ever."

"Doc." Jack returned. "That bowtie still looks ridiculous."

"Oi, its cool!"

"Okay." Jack looked back at Shepard. "All I care about right now is getting my guys out of here."

"Your guys?" Shepard smiled.

Jack looked up at the students. "Yeah. I guess so."

"I can't think of anyone who would care about them more." Shepard told her.

"Well, I had some free time while you were off playing hero." Jack said. "The Alliance knew I helped you. They offered me this, and apparently the students responded well to my teaching style." Jack raised her voice for the last part, so her students could hear.

"The psychotic biotic!" A male student reaponded.

"'I will destroy you!'" A female one shouted.

"Drink your juice, Rodruigez!" Jack retorted. "You couldn't destroy wet tissue paper!"

 _"Cortez to extraction team."_ The Lieutenant radioed. _"The Cerberus cruiser's comin' back."_

Shepard looked at Jack and the students, and paused briefly. "Get back to the Normandy, Cortez. We'll find an alternate route off the station."

 _"Understood. Cortez out."_

"Shepard to Sanders." Shepard radioed. "The shuttle's a no-go. We'll need to find another way off the station."

 _"Understood."_ The woman responded. _"I can probably find another way, but I'll need station-wide camera access. Cerberus locked it down, but their control terminal's in Orion Hall, can you find it?"_

Shepard looked around, and saw a laptop sitting on a bench. She walked over to it, and disabled the lockout.

 _"Got it. Okay, if we can get to the shuttlebay and commandeer a Cerberus shuttle, that should give us an escape route. The fastest way to the shutlebay is through the Atrium."_

"Understood." Shepard responded. "We'll give the students a little time to regroup, and then we'll head out."

The Doctor took that moment to butt in. "Tell me, Kahlee, do you have access to ths station's door controls?"

 _"No, that's routed through a different systwm."_

The Doctor whipped out the sonic screwdriver, and used it on the terminal. "There, try it now."

 _"I have full control. How did you...?"_

"Trade secret." The Doctor winked at a camera. "Can you lock down all the doors alongside the path?"

A short pause occured. _"Done. That hasn't taken care of the Cerberus troops already in your way, but it should prevent them from calling in reinforcements. I'll get to the shuttles ahead of you and get a pair ready to fly."_

"Roger that." Shepard responded. "We'll meet you there." Shepard turned to Jack and the students. "Everyone be ready to go. We'll head in first, and draw their fire."

Jack nodded. "We'll shadow you on the second level and hit those fu..." Jack cut herself off, and cringed. "Those guys from above."

Shepard raised an eyebrow, but chose not to ask.

"Good plan." The Doctor complimented. "Keeps them out of the line of fire, too."

Shepard nodded, and addressed Jack. "Just time your shots and stay safe."

Jack turned to her students. "All right, I didn't bust my ass training you so you can die now. Keep low, pick your targets."

At that moment, the Cerberus announcer chose to address the students by sending the message to their omni-tools.

As the announcer prattled on, the Doctor rolled his eyes, and took the sonic, aiming it at the students. The announcer's voice suddenly cut out.

"There. Now can we go?" The Doctor asked. "Mean Girls comes on later and I promised Susan I'd watch it with her."

"Let's go." Shepard said, taking her assault rifle off her back, leading the team forth. The door sealed behind them, and the team pushed forward.

The door to the atrium opened, and the team charged ahead.

"Careful, it's another one of those mechs!" James pointed out.

"Just like last time!" Shepard commanded.

Garrus and EDI hit the mech with overloads, allowing the Doctor to pop up and jam its weapons, allowing the rest of the squad to open fire and unleash an array of warps, incineration blasts, and carnage shots at it, taking the mech out.

Now, there were only the regular Cerberus troopers and Engineers to fight. The team pushed forth, cutting through the resistance Cerberus put up. Combat Engineers tried to place down turrets, which the sonic screwdriver made short work of, while Jack and her student unleashed biotic attacks on the Guardians and Centurions from above.

Shepard's team cut through a side hall, to the other side of the atrium, pushing foward towards the shuttle bay.

"Jack, we're pushing ahead to the shuttlebay." Shepard radioed.

 _"Got it. We'll see you there."_

The team proceeded into one of the hallways, heading closer to the shuttlebay.

However, as they proceeded along, they ran into a group of Cerberus troopers attempting to get to yet another student. Well, group of students. These three were inside a shield bubble.

Shepard didn't hesitate to biotically charge forward into one of the troopers. She then slammed the ground with a nova, taking care of the other two.

Shepard caught her breath, and addressed the student. "I'm Commander Shepard, I'm here to help."

The student frowned. "I didn't buy it from the last guy, I'm not going to buy it now!"

"The square root of 906.01 equals..." A male student muttured from where he was working on the shield generator.

"30.1." Shepard finished for him.

The student looked up, and smiled slightly. "Hello, Commander Shepard."

Shepard smiled back. "David."

"You know her?" One of the students asked David.

"Yes." David answered. "She saved me, made it quiet."

The students dropped the shield, and David stood up.

"The biotic students are up that way." Shepard pointed. "Stick with them, they'll get you to safety."

The other two students nodded, and walked off, but David stayed behind.

He looked the squad over, stopping to look at EDI. "I recognize you. You're the Normandy's computer. I am... sorry."

"Don't be." EDI responded. "You were not at fault."

"Thank you." David smiled.

"Has Grissom Academy treated you alright?" Shepard asked.

"Yes." David nodded. "I've been counting."

"Anything in particular?" Shepard asked.

"The number of days you lengthened my life." David answered. "Thank you, Shepard."

"You're very welcome, David." Shepard responded. "You should go join your friends."

"I will." David nodded, and followed the path of the other two students.

"Who was that?" The Doctor inquired once David was out of earshot.

"David Archer." Shepard answered. "I'll tell you more after we get out of here. It's... a damn long story."

Shepard and the team continued forth, towards the shuttle bay. But in the room before the shuttle bay, there was a fully operational, and abandoned, ATLAS mech ripe for the taking.

"Shotgun." Shepard called.

"Fuck." James cursed.

Shepard walked over to the mech, and climbed inside. The canopy closed, and Shepard twisted the control sticks experimentally. Shepard pushed forward on the sticks, and the mech began walking forward, up the steps.

The team walked into the shuttlebay lobby, and Cerberus troops began to pour in from the sides.

"Aw yeah!" Shepard yelled as she began firing the mech's gun on the Cerberus troops. "How's this taste assholes!?"

Jack began sending over the students over in groups, while Shepard and the team drew the fire off them.

"Scratch one!" Garrus yelled, as he put a sniper round through the viewing slot of a guardian's shield.

"Like fish in a barrel!" Vega shouted, dropping a Centurion.

"Still don't know what that means!" Garrus returned.

 _"The shuttles are almost ready for take-off._ " Kahlee announced over the loudspeaker.

Jack sent over the second group, and another ATLAS entered the room.

Shepard marched her mech over to the other, raised one of the mech's arms, and bought it down on the other's head, taking down the shields, and cracking the canopy.

Shepard stepped back, and fired a rocket at the mech, shattering the canopy fully, and damaging the mech beyond repair.

 _"The shuttles are ready, we have to leave now!"_ Kahlee announced.

With the threat dealt with, Shepard hopped out, and led the team into the shuttlebay proper, Cerberus hot on thier heels. Jack ushered each and every one of the students on the shuttles, and only then did she hop aboard.

Shepard and the team followed suit, and with everyone on the shuttles, the bay doors opened, and the two commandeered Cerberus shuttles departed Grissom Academy for good.


End file.
